HEADER IMMUNE SYSTEM 15-APR-24 8Z3A TITLE CRYSTAL STRUCTURE OF SONIC HEDGEHOG IN COMPLEX WITH ANTIBODY 5E1 TITLE 2 WITHOUT METALS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SONIC HEDGEHOG PROTEIN N-PRODUCT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SHHN,SHH N-TERMINAL PROCESSED SIGNALING DOMAINS,SHHNP; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEAVY CHAIN OF ANTIBODY 5E1; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF ANTIBODY 5E1; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SHH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: IGG; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: EXPI293; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 GENE: IGG; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: EXPI293 KEYWDS SONIC HEDGEHOG PROTEIN (SHH), ANTIBODY, FLEXIBLE/FLUCTUATED EPITOPE, KEYWDS 2 AFFINITY IMPROVEMENT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,I.KANEDA,K.TSUMOTO REVDAT 1 16-APR-25 8Z3A 0 JRNL AUTH I.KANEDA,R.MATSUNAGA,S.NAGATOISHI,A.SENOO,J.M.M.CAAVEIRO, JRNL AUTH 2 D.KURODA,K.TSUMOTO JRNL TITL BIOPHYSICAL INSIGHTS TO IMPROVE AFFINITY OF ANTIBODIES TO JRNL TITL 2 FLUCTUATED EPITOPE OF ANTIGEN: A CASE OF ANTI-SHH ANTIBODY JRNL TITL 3 5E1 AGAINST SHH ANTIGEN. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 72234 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3093 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5248 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 229 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4467 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 572 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 0.83000 REMARK 3 B33 (A**2) : -0.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.827 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4681 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4218 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6378 ; 1.825 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9857 ; 1.457 ; 1.577 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 598 ; 7.764 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 227 ;33.019 ;23.040 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 781 ;13.867 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.228 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 616 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5255 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 967 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2327 ; 1.162 ; 1.474 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2326 ; 1.162 ; 1.473 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2910 ; 1.840 ; 2.203 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2911 ; 1.839 ; 2.204 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2354 ; 1.699 ; 1.673 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2352 ; 1.697 ; 1.673 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3453 ; 2.721 ; 2.420 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5273 ; 5.269 ;18.318 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5274 ; 5.269 ;18.325 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 39 A 188 REMARK 3 ORIGIN FOR THE GROUP (A): -1.5517 -23.9202 -0.0028 REMARK 3 T TENSOR REMARK 3 T11: 0.0112 T22: 0.0347 REMARK 3 T33: 0.0351 T12: 0.0154 REMARK 3 T13: -0.0025 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 4.3753 L22: 1.8448 REMARK 3 L33: 2.3102 L12: -0.5699 REMARK 3 L13: 0.5272 L23: -0.8797 REMARK 3 S TENSOR REMARK 3 S11: 0.0577 S12: 0.1095 S13: -0.3212 REMARK 3 S21: -0.0747 S22: -0.0134 S23: 0.1534 REMARK 3 S31: 0.0964 S32: 0.0157 S33: -0.0443 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 219 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2695 -14.1882 -39.1737 REMARK 3 T TENSOR REMARK 3 T11: 0.0074 T22: 0.0108 REMARK 3 T33: 0.0460 T12: 0.0030 REMARK 3 T13: 0.0018 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.1241 L22: 0.9572 REMARK 3 L33: 3.2220 L12: -0.1945 REMARK 3 L13: -0.2855 L23: 0.7947 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: -0.0196 S13: -0.1066 REMARK 3 S21: -0.0345 S22: -0.0599 S23: 0.0567 REMARK 3 S31: 0.0142 S32: -0.1084 S33: 0.1228 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 211 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0910 -26.9716 -42.7316 REMARK 3 T TENSOR REMARK 3 T11: 0.0814 T22: 0.0803 REMARK 3 T33: 0.0493 T12: 0.0550 REMARK 3 T13: 0.0268 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 0.4906 L22: 0.1949 REMARK 3 L33: 2.8980 L12: -0.0185 REMARK 3 L13: -0.2540 L23: 0.7064 REMARK 3 S TENSOR REMARK 3 S11: -0.0995 S12: -0.0053 S13: -0.1261 REMARK 3 S21: -0.0077 S22: -0.0054 S23: 0.0098 REMARK 3 S31: 0.1319 S32: 0.1256 S33: 0.1049 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8Z3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.2.2 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75399 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 53.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.94300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM KNO3, 20% PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 34.68500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.42500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.42500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.68500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.99500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 29 REMARK 465 PHE A 30 REMARK 465 GLY A 31 REMARK 465 LYS A 32 REMARK 465 ARG A 33 REMARK 465 ARG A 34 REMARK 465 HIS A 35 REMARK 465 PRO A 36 REMARK 465 LYS A 37 REMARK 465 LYS A 38 REMARK 465 ASN A 189 REMARK 465 SER A 190 REMARK 465 VAL A 191 REMARK 465 ALA A 192 REMARK 465 ALA A 193 REMARK 465 LYS A 194 REMARK 465 SER A 195 REMARK 465 GLY A 196 REMARK 465 GLY A 197 REMARK 465 SER H 133 REMARK 465 SER H 134 REMARK 465 LYS H 135 REMARK 465 SER H 136 REMARK 465 THR H 137 REMARK 465 SER H 138 REMARK 465 LYS H 220 REMARK 465 GLU H 221 REMARK 465 GLN H 222 REMARK 465 LYS H 223 REMARK 465 LEU H 224 REMARK 465 ILE H 225 REMARK 465 SER H 226 REMARK 465 GLU H 227 REMARK 465 GLU H 228 REMARK 465 ASP H 229 REMARK 465 LEU H 230 REMARK 465 ASN H 231 REMARK 465 SER H 232 REMARK 465 ALA H 233 REMARK 465 VAL H 234 REMARK 465 ASP H 235 REMARK 465 HIS H 236 REMARK 465 HIS H 237 REMARK 465 HIS H 238 REMARK 465 HIS H 239 REMARK 465 HIS H 240 REMARK 465 HIS H 241 REMARK 465 GLY L 212 REMARK 465 GLU L 213 REMARK 465 CYS L 214 REMARK 465 GLU L 215 REMARK 465 GLN L 216 REMARK 465 LYS L 217 REMARK 465 LEU L 218 REMARK 465 ILE L 219 REMARK 465 SER L 220 REMARK 465 GLU L 221 REMARK 465 GLU L 222 REMARK 465 ASP L 223 REMARK 465 LEU L 224 REMARK 465 ASN L 225 REMARK 465 SER L 226 REMARK 465 ALA L 227 REMARK 465 VAL L 228 REMARK 465 ASP L 229 REMARK 465 HIS L 230 REMARK 465 HIS L 231 REMARK 465 HIS L 232 REMARK 465 HIS L 233 REMARK 465 HIS L 234 REMARK 465 HIS L 235 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 89 O HOH A 201 2.16 REMARK 500 OD2 ASP L 17 O HOH L 401 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU H 154 CD GLU H 154 OE2 0.083 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP L 60 CB - CA - C ANGL. DEV. = -13.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 58 -117.65 -110.64 REMARK 500 SER H 44 -126.47 43.90 REMARK 500 GLU H 101 35.06 73.68 REMARK 500 ASP H 150 62.72 71.25 REMARK 500 SER H 194 49.37 -78.60 REMARK 500 LEU H 195 -67.78 -107.78 REMARK 500 THR H 197 -74.88 -64.55 REMARK 500 SER L 30 -130.62 52.60 REMARK 500 ALA L 51 -34.44 70.37 REMARK 500 ALA L 84 170.66 177.50 REMARK 500 LYS L 169 -71.57 -78.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE H 105 PHE H 106 -146.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Z3A A 29 197 UNP Q15465 SHH_HUMAN 29 197 DBREF 8Z3A H 1 241 PDB 8Z3A 8Z3A 1 241 DBREF 8Z3A L 1 235 PDB 8Z3A 8Z3A 1 235 SEQRES 1 A 169 GLY PHE GLY LYS ARG ARG HIS PRO LYS LYS LEU THR PRO SEQRES 2 A 169 LEU ALA TYR LYS GLN PHE ILE PRO ASN VAL ALA GLU LYS SEQRES 3 A 169 THR LEU GLY ALA SER GLY ARG TYR GLU GLY LYS ILE SER SEQRES 4 A 169 ARG ASN SER GLU ARG PHE LYS GLU LEU THR PRO ASN TYR SEQRES 5 A 169 ASN PRO ASP ILE ILE PHE LYS ASP GLU GLU ASN THR GLY SEQRES 6 A 169 ALA ASP ARG LEU MET THR GLN ARG CYS LYS ASP LYS LEU SEQRES 7 A 169 ASN ALA LEU ALA ILE SER VAL MET ASN GLN TRP PRO GLY SEQRES 8 A 169 VAL LYS LEU ARG VAL THR GLU GLY TRP ASP GLU ASP GLY SEQRES 9 A 169 HIS HIS SER GLU GLU SER LEU HIS TYR GLU GLY ARG ALA SEQRES 10 A 169 VAL ASP ILE THR THR SER ASP ARG ASP ARG SER LYS TYR SEQRES 11 A 169 GLY MET LEU ALA ARG LEU ALA VAL GLU ALA GLY PHE ASP SEQRES 12 A 169 TRP VAL TYR TYR GLU SER LYS ALA HIS ILE HIS CYS SER SEQRES 13 A 169 VAL LYS ALA GLU ASN SER VAL ALA ALA LYS SER GLY GLY SEQRES 1 H 241 GLN VAL GLN LEU GLN GLN SER GLY PRO GLU LEU VAL ARG SEQRES 2 H 241 PRO GLY VAL SER VAL LYS ILE SER CYS LYS GLY SER GLY SEQRES 3 H 241 TYR THR PHE ILE ASP GLU ALA LEU HIS TRP VAL LYS GLN SEQRES 4 H 241 SER HIS ALA GLU SER LEU GLU TRP ILE GLY VAL ILE ARG SEQRES 5 H 241 PRO TYR SER GLY GLU THR ASN TYR ASN GLN LYS PHE LYS SEQRES 6 H 241 ASP LYS ALA THR MET THR VAL ASP ILE SER SER SER THR SEQRES 7 H 241 ALA TYR LEU GLU LEU ALA ARG LEU THR SER GLU ASP SER SEQRES 8 H 241 ALA ILE TYR TYR CYS ALA ARG ASP TRP GLU ARG GLY ASP SEQRES 9 H 241 PHE PHE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 241 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 241 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 241 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 241 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 241 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 241 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 241 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 241 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS GLU SEQRES 18 H 241 GLN LYS LEU ILE SER GLU GLU ASP LEU ASN SER ALA VAL SEQRES 19 H 241 ASP HIS HIS HIS HIS HIS HIS SEQRES 1 L 235 ASP ILE VAL MET THR GLN THR PRO LYS PHE LEU LEU VAL SEQRES 2 L 235 SER ALA GLY ASP LYS VAL THR ILE THR CYS LYS ALA SER SEQRES 3 L 235 GLN SER VAL SER ASN ASP LEU THR TRP TYR GLN GLN LYS SEQRES 4 L 235 PRO GLY GLN SER PRO LYS LEU LEU ILE TYR TYR ALA SER SEQRES 5 L 235 ASN ARG TYR THR GLY VAL PRO ASP ARG PHE THR GLY SER SEQRES 6 L 235 GLY TYR GLY THR ASP PHE THR PHE THR ILE SER THR VAL SEQRES 7 L 235 GLN ALA GLU ASP LEU ALA VAL TYR PHE CYS GLN GLN ASP SEQRES 8 L 235 TYR GLY SER PRO PRO THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 235 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 235 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 235 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 235 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 235 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 235 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 235 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 235 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 235 PHE ASN ARG GLY GLU CYS GLU GLN LYS LEU ILE SER GLU SEQRES 18 L 235 GLU ASP LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS SEQRES 19 L 235 HIS HET GOL H 301 6 HET NO3 L 301 4 HETNAM GOL GLYCEROL HETNAM NO3 NITRATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 NO3 N O3 1- FORMUL 6 HOH *572(H2 O) HELIX 1 AA1 GLU A 71 LEU A 76 5 6 HELIX 2 AA2 GLY A 93 ASP A 95 5 3 HELIX 3 AA3 THR A 99 TRP A 117 1 19 HELIX 4 AA4 SER A 138 GLY A 143 5 6 HELIX 5 AA5 ASP A 154 SER A 156 5 3 HELIX 6 AA6 LYS A 157 GLY A 169 1 13 HELIX 7 AA7 THR H 28 GLU H 32 5 5 HELIX 8 AA8 GLN H 62 LYS H 65 5 4 HELIX 9 AA9 ILE H 74 SER H 76 5 3 HELIX 10 AB1 THR H 87 SER H 91 5 5 HELIX 11 AB2 SER H 162 ALA H 164 5 3 HELIX 12 AB3 LYS H 207 ASN H 210 5 4 HELIX 13 AB4 GLN L 79 LEU L 83 5 5 HELIX 14 AB5 SER L 121 SER L 127 1 7 HELIX 15 AB6 LYS L 183 LYS L 188 1 6 SHEET 1 AA1 6 PHE A 47 ILE A 48 0 SHEET 2 AA1 6 TRP A 172 SER A 177 -1 O VAL A 173 N ILE A 48 SHEET 3 AA1 6 HIS A 180 SER A 184 -1 O HIS A 182 N TYR A 174 SHEET 4 AA1 6 ALA A 145 THR A 150 -1 N VAL A 146 O CYS A 183 SHEET 5 AA1 6 LEU A 122 GLU A 126 -1 N GLU A 126 O ASP A 147 SHEET 6 AA1 6 ILE A 84 PHE A 86 1 N ILE A 85 O VAL A 124 SHEET 1 AA2 2 THR A 77 PRO A 78 0 SHEET 2 AA2 2 LEU A 97 MET A 98 -1 O MET A 98 N THR A 77 SHEET 1 AA3 4 GLN H 3 GLN H 6 0 SHEET 2 AA3 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 AA3 4 THR H 78 LEU H 83 -1 O LEU H 81 N ILE H 20 SHEET 4 AA3 4 ALA H 68 ASP H 73 -1 N ASP H 73 O THR H 78 SHEET 1 AA4 6 GLU H 10 VAL H 12 0 SHEET 2 AA4 6 THR H 113 VAL H 117 1 O THR H 116 N GLU H 10 SHEET 3 AA4 6 ALA H 92 ARG H 98 -1 N ALA H 92 O VAL H 115 SHEET 4 AA4 6 LEU H 34 SER H 40 -1 N HIS H 35 O ALA H 97 SHEET 5 AA4 6 SER H 44 ILE H 51 -1 O ILE H 48 N TRP H 36 SHEET 6 AA4 6 THR H 58 TYR H 60 -1 O ASN H 59 N VAL H 50 SHEET 1 AA5 4 GLU H 10 VAL H 12 0 SHEET 2 AA5 4 THR H 113 VAL H 117 1 O THR H 116 N GLU H 10 SHEET 3 AA5 4 ALA H 92 ARG H 98 -1 N ALA H 92 O VAL H 115 SHEET 4 AA5 4 TYR H 108 TRP H 109 -1 O TYR H 108 N ARG H 98 SHEET 1 AA6 4 SER H 126 LEU H 130 0 SHEET 2 AA6 4 THR H 141 TYR H 151 -1 O LEU H 147 N PHE H 128 SHEET 3 AA6 4 TYR H 182 PRO H 191 -1 O LEU H 184 N VAL H 148 SHEET 4 AA6 4 VAL H 169 THR H 171 -1 N HIS H 170 O VAL H 187 SHEET 1 AA7 4 SER H 126 LEU H 130 0 SHEET 2 AA7 4 THR H 141 TYR H 151 -1 O LEU H 147 N PHE H 128 SHEET 3 AA7 4 TYR H 182 PRO H 191 -1 O LEU H 184 N VAL H 148 SHEET 4 AA7 4 VAL H 175 LEU H 176 -1 N VAL H 175 O SER H 183 SHEET 1 AA8 3 THR H 157 TRP H 160 0 SHEET 2 AA8 3 ILE H 201 HIS H 206 -1 O ASN H 203 N SER H 159 SHEET 3 AA8 3 THR H 211 LYS H 216 -1 O VAL H 213 N VAL H 204 SHEET 1 AA9 4 MET L 4 THR L 7 0 SHEET 2 AA9 4 VAL L 19 ALA L 25 -1 O THR L 22 N THR L 7 SHEET 3 AA9 4 ASP L 70 ILE L 75 -1 O PHE L 73 N ILE L 21 SHEET 4 AA9 4 PHE L 62 GLY L 66 -1 N THR L 63 O THR L 74 SHEET 1 AB1 6 PHE L 10 SER L 14 0 SHEET 2 AB1 6 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 AB1 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB1 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 AB1 6 LYS L 45 TYR L 49 -1 O ILE L 48 N TRP L 35 SHEET 6 AB1 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AB2 4 PHE L 10 SER L 14 0 SHEET 2 AB2 4 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 AB2 4 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB2 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB3 4 SER L 114 PHE L 118 0 SHEET 2 AB3 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 AB3 4 TYR L 173 SER L 182 -1 O SER L 177 N CYS L 134 SHEET 4 AB3 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB4 4 ALA L 153 LEU L 154 0 SHEET 2 AB4 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB4 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB4 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 2 CYS H 146 CYS H 202 1555 1555 2.05 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.14 SSBOND 4 CYS L 134 CYS L 194 1555 1555 1.97 CISPEP 1 ILE A 48 PRO A 49 0 -4.51 CISPEP 2 ILE A 48 PRO A 49 0 -4.23 CISPEP 3 PHE H 152 PRO H 153 0 -12.01 CISPEP 4 GLU H 154 PRO H 155 0 -3.47 CISPEP 5 THR L 7 PRO L 8 0 -11.14 CISPEP 6 SER L 94 PRO L 95 0 2.11 CISPEP 7 TYR L 140 PRO L 141 0 1.54 CRYST1 69.370 83.990 126.850 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007883 0.00000