HEADER IMMUNE SYSTEM 14-DEC-24 9L1K TITLE SDABA YERLS MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SDABA YERLS MUTANT; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL1; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DE3 KEYWDS SINGLE DOMAIN ANTIBODY, MUTAGENESIS, STABILITY, FRAMEWORK REGION, KEYWDS 2 VHH, ALPACA ANTIBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,J.FERNANDEZ-PEREZ,K.TSUMOTO REVDAT 1 27-AUG-25 9L1K 0 JRNL AUTH Y.UTO,M.NAKAKIDO,T.YOKOO,J.FERNANDEZ-PEREZ,K.ENTZMINGER, JRNL AUTH 2 T.MARUYAMA,C.J.OKUMURA,D.KURODA,J.M.M.CAAVEIRO,K.TSUMOTO JRNL TITL IMPROVING THE SOLUBILITY OF SINGLE DOMAIN ANTIBODIES USING JRNL TITL 2 VH-LIKE HALLMARK RESIDUES. JRNL REF PROTEIN SCI. V. 34 70189 2025 JRNL REFN ESSN 1469-896X JRNL PMID 40521627 JRNL DOI 10.1002/PRO.70189 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 93061 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.959 REMARK 3 FREE R VALUE TEST SET COUNT : 4615 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 355 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3720 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 582 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.30300 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : -0.67300 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.061 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.561 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3932 ; 0.006 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3505 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5315 ; 1.507 ; 1.810 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8084 ; 0.527 ; 1.758 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 501 ; 7.282 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ;10.338 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 632 ;12.172 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 543 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4790 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 986 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 629 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 69 ; 0.220 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1812 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 392 ; 0.227 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.246 ; 0.200 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): 1983 ; 4.672 ; 2.066 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1983 ; 4.662 ; 2.065 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2488 ; 7.083 ; 3.708 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2489 ; 7.086 ; 3.709 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1949 ; 6.243 ; 2.312 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1950 ; 6.241 ; 2.313 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2826 ; 9.015 ; 4.098 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2827 ; 9.013 ; 4.098 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7437 ; 2.821 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9L1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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 : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.13 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93118 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 47.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 30% PEG 4000, REMARK 280 PH 7.4, VAPOR DIFFUSION, HANGING 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 26.19650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.96900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.62550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.96900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.19650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.62550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 HIS C 126 REMARK 465 HIS D 122 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 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 O HOH D 351 O HOH D 362 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLY D 55 O HOH C 407 1455 2.16 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 CYS B 96 CB - CA - C ANGL. DEV. = 9.5 DEGREES REMARK 500 CYS D 96 CB - CA - C ANGL. DEV. = 11.1 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 B 92 167.72 179.83 REMARK 500 ALA C 92 166.24 178.68 REMARK 500 TYR D 59 142.39 -174.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 101 0.20 SIDE CHAIN REMARK 500 ARG B 99 0.10 SIDE CHAIN REMARK 500 ARG C 99 0.07 SIDE CHAIN REMARK 500 ARG D 101 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 452 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH B 453 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH C 433 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH D 443 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH D 444 DISTANCE = 6.67 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 33 O REMARK 620 2 ARG A 99 O 145.3 REMARK 620 3 HOH A 377 O 92.0 99.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER D 30 O REMARK 620 2 THR D 53 O 123.6 REMARK 620 N 1 DBREF 9L1K A 1 126 PDB 9L1K 9L1K 1 126 DBREF 9L1K B 1 126 PDB 9L1K 9L1K 1 126 DBREF 9L1K C 1 126 PDB 9L1K 9L1K 1 126 DBREF 9L1K D 1 126 PDB 9L1K 9L1K 1 126 SEQRES 1 A 126 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 A 126 PRO GLY GLY SER LEU LYS LEU SER CYS LYS THR SER GLY SEQRES 3 A 126 PHE THR PHE SER SER TYR TRP MET TYR TRP TYR ARG GLN SEQRES 4 A 126 ALA PRO GLY LYS GLU ARG GLU LEU VAL SER GLY ILE ASN SEQRES 5 A 126 THR GLY GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 126 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 126 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 126 ALA VAL TYR TYR CYS ALA ARG ARG ASP ARG GLY GLY MET SEQRES 9 A 126 ASP TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER SEQRES 10 A 126 ALA ALA GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 126 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 B 126 PRO GLY GLY SER LEU LYS LEU SER CYS LYS THR SER GLY SEQRES 3 B 126 PHE THR PHE SER SER TYR TRP MET TYR TRP TYR ARG GLN SEQRES 4 B 126 ALA PRO GLY LYS GLU ARG GLU LEU VAL SER GLY ILE ASN SEQRES 5 B 126 THR GLY GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 126 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 126 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 126 ALA VAL TYR TYR CYS ALA ARG ARG ASP ARG GLY GLY MET SEQRES 9 B 126 ASP TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER SEQRES 10 B 126 ALA ALA GLY HIS HIS HIS HIS HIS HIS SEQRES 1 C 126 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 C 126 PRO GLY GLY SER LEU LYS LEU SER CYS LYS THR SER GLY SEQRES 3 C 126 PHE THR PHE SER SER TYR TRP MET TYR TRP TYR ARG GLN SEQRES 4 C 126 ALA PRO GLY LYS GLU ARG GLU LEU VAL SER GLY ILE ASN SEQRES 5 C 126 THR GLY GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 C 126 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 C 126 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 C 126 ALA VAL TYR TYR CYS ALA ARG ARG ASP ARG GLY GLY MET SEQRES 9 C 126 ASP TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER SEQRES 10 C 126 ALA ALA GLY HIS HIS HIS HIS HIS HIS SEQRES 1 D 126 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 D 126 PRO GLY GLY SER LEU LYS LEU SER CYS LYS THR SER GLY SEQRES 3 D 126 PHE THR PHE SER SER TYR TRP MET TYR TRP TYR ARG GLN SEQRES 4 D 126 ALA PRO GLY LYS GLU ARG GLU LEU VAL SER GLY ILE ASN SEQRES 5 D 126 THR GLY GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 D 126 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 D 126 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 126 ALA VAL TYR TYR CYS ALA ARG ARG ASP ARG GLY GLY MET SEQRES 9 D 126 ASP TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER SEQRES 10 D 126 ALA ALA GLY HIS HIS HIS HIS HIS HIS HET SO4 A 201 5 HET NA A 202 1 HET SO4 B 201 5 HET SO4 B 202 5 HET SO4 C 201 5 HET GOL C 202 6 HET SO4 D 201 5 HET SO4 D 202 5 HET SO4 D 203 5 HET SO4 D 204 5 HET GOL D 205 6 HET GOL D 206 6 HET NA D 207 1 HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 8(O4 S 2-) FORMUL 6 NA 2(NA 1+) FORMUL 10 GOL 3(C3 H8 O3) FORMUL 18 HOH *582(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 LYS A 87 THR A 91 5 5 HELIX 3 AA3 THR B 28 TYR B 32 5 5 HELIX 4 AA4 LYS B 87 THR B 91 5 5 HELIX 5 AA5 THR C 28 TYR C 32 5 5 HELIX 6 AA6 ASP C 62 LYS C 65 5 4 HELIX 7 AA7 LYS C 87 THR C 91 5 5 HELIX 8 AA8 THR D 28 TYR D 32 5 5 HELIX 9 AA9 ASP D 62 LYS D 65 5 4 HELIX 10 AB1 LYS D 87 THR D 91 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA2 6 ALA A 92 ARG A 98 -1 N TYR A 94 O THR A 111 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N TYR A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 SER A 57 TYR A 60 -1 O THR A 58 N GLY A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA3 4 ALA A 92 ARG A 98 -1 N TYR A 94 O THR A 111 SHEET 4 AA3 4 TYR A 106 TRP A 107 -1 O TYR A 106 N ARG A 98 SHEET 1 AA4 4 GLN B 3 SER B 7 0 SHEET 2 AA4 4 LEU B 18 SER B 25 -1 O LYS B 23 N VAL B 5 SHEET 3 AA4 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA4 4 PHE B 68 ASP B 73 -1 N ASP B 73 O THR B 78 SHEET 1 AA5 6 GLY B 10 VAL B 12 0 SHEET 2 AA5 6 THR B 111 VAL B 115 1 O THR B 114 N VAL B 12 SHEET 3 AA5 6 ALA B 92 ARG B 99 -1 N TYR B 94 O THR B 111 SHEET 4 AA5 6 MET B 34 GLN B 39 -1 N TYR B 37 O TYR B 95 SHEET 5 AA5 6 GLU B 46 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 AA5 6 SER B 57 TYR B 60 -1 O THR B 58 N GLY B 50 SHEET 1 AA6 4 GLY B 10 VAL B 12 0 SHEET 2 AA6 4 THR B 111 VAL B 115 1 O THR B 114 N VAL B 12 SHEET 3 AA6 4 ALA B 92 ARG B 99 -1 N TYR B 94 O THR B 111 SHEET 4 AA6 4 ASP B 105 TRP B 107 -1 O TYR B 106 N ARG B 98 SHEET 1 AA7 4 GLN C 3 SER C 7 0 SHEET 2 AA7 4 LEU C 18 SER C 25 -1 O SER C 21 N SER C 7 SHEET 3 AA7 4 THR C 78 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AA7 4 PHE C 68 ASP C 73 -1 N ASP C 73 O THR C 78 SHEET 1 AA8 6 GLY C 10 VAL C 12 0 SHEET 2 AA8 6 THR C 111 VAL C 115 1 O THR C 114 N GLY C 10 SHEET 3 AA8 6 ALA C 92 ARG C 99 -1 N TYR C 94 O THR C 111 SHEET 4 AA8 6 MET C 34 GLN C 39 -1 N TYR C 37 O TYR C 95 SHEET 5 AA8 6 GLU C 46 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 AA8 6 SER C 57 TYR C 60 -1 O THR C 58 N GLY C 50 SHEET 1 AA9 4 GLY C 10 VAL C 12 0 SHEET 2 AA9 4 THR C 111 VAL C 115 1 O THR C 114 N GLY C 10 SHEET 3 AA9 4 ALA C 92 ARG C 99 -1 N TYR C 94 O THR C 111 SHEET 4 AA9 4 ASP C 105 TRP C 107 -1 O TYR C 106 N ARG C 98 SHEET 1 AB1 4 GLN D 3 SER D 7 0 SHEET 2 AB1 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AB1 4 THR D 78 MET D 83 -1 O LEU D 81 N LEU D 20 SHEET 4 AB1 4 PHE D 68 ASP D 73 -1 N THR D 69 O GLN D 82 SHEET 1 AB2 6 GLY D 10 VAL D 12 0 SHEET 2 AB2 6 THR D 111 VAL D 115 1 O THR D 114 N GLY D 10 SHEET 3 AB2 6 ALA D 92 ARG D 99 -1 N TYR D 94 O THR D 111 SHEET 4 AB2 6 MET D 34 GLN D 39 -1 N TYR D 37 O TYR D 95 SHEET 5 AB2 6 GLU D 46 ILE D 51 -1 O GLU D 46 N ARG D 38 SHEET 6 AB2 6 SER D 57 TYR D 60 -1 O THR D 58 N GLY D 50 SHEET 1 AB3 4 GLY D 10 VAL D 12 0 SHEET 2 AB3 4 THR D 111 VAL D 115 1 O THR D 114 N GLY D 10 SHEET 3 AB3 4 ALA D 92 ARG D 99 -1 N TYR D 94 O THR D 111 SHEET 4 AB3 4 ASP D 105 TRP D 107 -1 O TYR D 106 N ARG D 98 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.08 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.02 SSBOND 3 CYS C 22 CYS C 96 1555 1555 2.11 SSBOND 4 CYS D 22 CYS D 96 1555 1555 1.98 LINK O TRP A 33 NA NA A 202 1555 1555 2.47 LINK O ARG A 99 NA NA A 202 1555 1555 2.18 LINK NA NA A 202 O HOH A 377 1555 1555 3.07 LINK O SER D 30 NA NA D 207 1555 1555 2.90 LINK O THR D 53 NA NA D 207 1555 1555 2.15 CRYST1 52.393 113.251 113.938 90.00 90.00 90.00 P 21 21 21 16 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 0.019087 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008777 0.00000