HEADER IMMUNE SYSTEM 07-APR-25 9UDN TITLE SINGLE-CHAIN FV ANTIBODY OF F8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-CHAIN FV ANTIBODY OF F8; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIGEN BINDING, AFFINITY MATURATION, SOMATIC HYPERMUTATION, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.YOSHIDA,Y.HANAZONO,N.NUMOTO,N.ITO,M.ODA REVDAT 1 05-NOV-25 9UDN 0 JRNL AUTH M.YOSHIDA,Y.HANAZONO,N.NUMOTO,S.YABUNO,N.ITO,T.AZUMA,M.ODA JRNL TITL STRUCTURAL BASIS OF ANTI-(4-HYDROXY-3-NITROPHENYL)ACETYL JRNL TITL 2 ANTIBODIES DURING AFFINITY MATURATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 19769 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.8000 - 3.4600 0.98 2756 145 0.1519 0.1906 REMARK 3 2 3.4600 - 2.7500 0.98 2679 141 0.1748 0.2167 REMARK 3 3 2.7500 - 2.4000 0.99 2696 143 0.1890 0.2339 REMARK 3 4 2.4000 - 2.1800 0.99 2674 140 0.1912 0.2243 REMARK 3 5 2.1800 - 2.0300 1.00 2696 141 0.1948 0.2286 REMARK 3 6 2.0200 - 1.9100 0.99 2685 142 0.2374 0.2591 REMARK 3 7 1.9100 - 1.8100 0.97 2595 136 0.2739 0.3482 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.236 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.015 1872 REMARK 3 ANGLE : 1.436 2554 REMARK 3 CHIRALITY : 0.104 280 REMARK 3 PLANARITY : 0.014 326 REMARK 3 DIHEDRAL : 17.369 667 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.5824 18.9338 13.3713 REMARK 3 T TENSOR REMARK 3 T11: 0.1939 T22: 0.1272 REMARK 3 T33: 0.1117 T12: 0.0186 REMARK 3 T13: -0.0279 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 2.1325 L22: 2.6180 REMARK 3 L33: 3.3692 L12: 0.0885 REMARK 3 L13: -1.1793 L23: -0.9945 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: -0.0565 S13: 0.0102 REMARK 3 S21: 0.0833 S22: -0.0497 S23: -0.1365 REMARK 3 S31: 0.1224 S32: 0.1697 S33: 0.0337 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1584 15.7328 8.4660 REMARK 3 T TENSOR REMARK 3 T11: 0.2165 T22: 0.4533 REMARK 3 T33: 0.5752 T12: 0.0997 REMARK 3 T13: 0.0723 T23: 0.1863 REMARK 3 L TENSOR REMARK 3 L11: 2.9085 L22: 1.0404 REMARK 3 L33: 2.8210 L12: -0.6452 REMARK 3 L13: -0.2043 L23: -1.1443 REMARK 3 S TENSOR REMARK 3 S11: -0.0535 S12: 0.3433 S13: 0.6177 REMARK 3 S21: -0.2972 S22: -0.4107 S23: -0.9337 REMARK 3 S31: 0.3932 S32: 0.8504 S33: 0.1206 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9UDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-25. REMARK 100 THE DEPOSITION ID IS D_1300058278. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-23 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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU 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 EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.54500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM PH 7.5, 1.4 M REMARK 280 SODIUM CITRATE TRIBASIC DIHYDRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.86500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.57000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.86500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.57000 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 301 LIES ON A SPECIAL POSITION. 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 119 REMARK 465 GLY A 120 REMARK 465 GLY A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 GLY A 125 REMARK 465 GLY A 126 REMARK 465 SER A 127 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 TYR A 36 49.14 39.09 REMARK 500 PRO A 44 150.46 -49.75 REMARK 500 ASP A 45 32.83 71.94 REMARK 500 THR A 55 -52.46 75.10 REMARK 500 TYR A 96 71.96 -117.74 REMARK 500 SER A 97 -47.25 70.40 REMARK 500 SER A 212 74.95 39.59 REMARK 500 TYR A 229 -1.22 70.80 REMARK 500 TYR A 230 -143.49 -120.49 REMARK 500 SER A 244 100.71 -58.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 9UDN A 1 245 PDB 9UDN 9UDN 1 245 SEQRES 1 A 245 GLY SER GLN ALA VAL VAL THR GLN GLU SER ALA LEU THR SEQRES 2 A 245 THR SER PRO GLY GLU THR VAL THR LEU THR CYS ARG SER SEQRES 3 A 245 SER THR GLY ALA VAL THR THR SER ASN TYR ALA ASN TRP SEQRES 4 A 245 VAL GLN GLU LYS PRO ASP HIS LEU PHE THR GLY LEU ILE SEQRES 5 A 245 GLY GLY THR ASN ASN ARG ALA PRO GLY VAL PRO ALA ARG SEQRES 6 A 245 PHE SER GLY SER LEU ILE GLY ASP LYS ALA ALA LEU THR SEQRES 7 A 245 ILE THR GLY ALA GLN THR GLU ASP GLU ALA ILE TYR PHE SEQRES 8 A 245 CYS ALA LEU TRP TYR SER ASN ARG TRP VAL PHE GLY GLY SEQRES 9 A 245 GLY THR LYS LEU THR VAL LEU GLY GLY GLY GLY GLY SER SEQRES 10 A 245 GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLN VAL GLN SEQRES 11 A 245 LEU GLN GLN PRO GLY ALA GLU LEU VAL LYS PRO GLY ALA SEQRES 12 A 245 SER VAL LYS LEU SER CYS LYS ALA SER GLY TYR THR PHE SEQRES 13 A 245 THR SER TYR TRP MET HIS TRP VAL LYS GLN ARG PRO GLY SEQRES 14 A 245 ARG GLY LEU GLU TRP ILE GLY ARG ILE ASP PRO ASN SER SEQRES 15 A 245 GLY GLY THR LYS TYR ASN GLU LYS PHE LYS SER LYS ALA SEQRES 16 A 245 THR LEU THR VAL ASP LYS PRO SER SER THR ALA TYR MET SEQRES 17 A 245 GLN LEU SER SER LEU THR SER GLU ASP SER ALA VAL TYR SEQRES 18 A 245 TYR CYS ALA ARG TYR ARG VAL TYR TYR ALA MET ASP TYR SEQRES 19 A 245 TRP GLY GLN GLY THR SER VAL THR VAL SER SER FORMUL 2 HOH *122(H2 O) HELIX 1 AA1 THR A 32 TYR A 36 5 5 HELIX 2 AA2 GLN A 83 GLU A 87 5 5 HELIX 3 AA3 THR A 155 TYR A 159 5 5 HELIX 4 AA4 GLU A 189 LYS A 192 5 4 HELIX 5 AA5 THR A 214 SER A 218 5 5 SHEET 1 AA1 4 VAL A 6 GLN A 8 0 SHEET 2 AA1 4 THR A 19 SER A 26 -1 O ARG A 25 N THR A 7 SHEET 3 AA1 4 LYS A 74 THR A 80 -1 O ILE A 79 N VAL A 20 SHEET 4 AA1 4 PHE A 66 ILE A 71 -1 N SER A 67 O THR A 78 SHEET 1 AA2 6 ALA A 11 THR A 14 0 SHEET 2 AA2 6 THR A 106 VAL A 110 1 O THR A 109 N THR A 14 SHEET 3 AA2 6 ALA A 88 TRP A 95 -1 N ALA A 88 O LEU A 108 SHEET 4 AA2 6 ASN A 38 LYS A 43 -1 N GLU A 42 O ILE A 89 SHEET 5 AA2 6 LEU A 47 GLY A 53 -1 O THR A 49 N GLN A 41 SHEET 6 AA2 6 ASN A 57 ARG A 58 -1 O ASN A 57 N GLY A 53 SHEET 1 AA3 4 ALA A 11 THR A 14 0 SHEET 2 AA3 4 THR A 106 VAL A 110 1 O THR A 109 N THR A 14 SHEET 3 AA3 4 ALA A 88 TRP A 95 -1 N ALA A 88 O LEU A 108 SHEET 4 AA3 4 TRP A 100 PHE A 102 -1 O VAL A 101 N LEU A 94 SHEET 1 AA4 4 GLN A 130 GLN A 132 0 SHEET 2 AA4 4 VAL A 145 SER A 152 -1 O LYS A 150 N GLN A 132 SHEET 3 AA4 4 THR A 205 LEU A 210 -1 O MET A 208 N LEU A 147 SHEET 4 AA4 4 ALA A 195 ASP A 200 -1 N THR A 198 O TYR A 207 SHEET 1 AA5 6 ALA A 136 VAL A 139 0 SHEET 2 AA5 6 THR A 239 VAL A 243 1 O SER A 240 N GLU A 137 SHEET 3 AA5 6 ALA A 219 TYR A 226 -1 N ALA A 219 O VAL A 241 SHEET 4 AA5 6 TRP A 160 ARG A 167 -1 N HIS A 162 O ALA A 224 SHEET 5 AA5 6 GLY A 171 ILE A 178 -1 O GLU A 173 N LYS A 165 SHEET 6 AA5 6 THR A 185 TYR A 187 -1 O LYS A 186 N ARG A 177 SHEET 1 AA6 4 ALA A 136 VAL A 139 0 SHEET 2 AA6 4 THR A 239 VAL A 243 1 O SER A 240 N GLU A 137 SHEET 3 AA6 4 ALA A 219 TYR A 226 -1 N ALA A 219 O VAL A 241 SHEET 4 AA6 4 MET A 232 TRP A 235 -1 O TYR A 234 N ARG A 225 SSBOND 1 CYS A 24 CYS A 92 1555 1555 2.11 SSBOND 2 CYS A 149 CYS A 223 1555 1555 2.04 CRYST1 135.730 35.140 46.450 90.00 99.63 90.00 C 1 2 1 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 0.007368 0.000000 0.001250 0.00000 SCALE2 0.000000 0.028458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021836 0.00000