HEADER IMMUNE SYSTEM 03-DEC-19 6LFV TITLE CRYSTAL STRUCTURE OF PCB4SCFV(HN56D) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PCB4SCFV(HN56D); 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 CO-PCB, ANTIBODY FRAGMENT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.YAMAGATA,H.MORIOKA REVDAT 2 22-NOV-23 6LFV 1 REMARK REVDAT 1 09-DEC-20 6LFV 0 JRNL AUTH T.NAKAMURA,H.MORIOKA JRNL TITL CRYSTAL STRUCTURE OF PCB4SCFV(HN56D) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 34655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1775 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 1.9500 - 1.9000 0.98 2496 156 0.2762 0.2858 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.712 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.15 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 : 0.002 1825 REMARK 3 ANGLE : 0.521 2475 REMARK 3 CHIRALITY : 0.042 278 REMARK 3 PLANARITY : 0.004 310 REMARK 3 DIHEDRAL : 13.719 658 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6LFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-16 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 32.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3ESU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG 8000, ETHYLENE GLYCOL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.21000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.91500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.21000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.91500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 46.21000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 26.91500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 46.21000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.91500 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 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 ARG A 109 REMARK 465 PRO A 110 REMARK 465 GLY A 111 REMARK 465 GLY A 112 REMARK 465 GLY A 113 REMARK 465 GLY A 114 REMARK 465 SER A 115 REMARK 465 GLY A 116 REMARK 465 GLY A 117 REMARK 465 GLY A 118 REMARK 465 GLY A 119 REMARK 465 SER A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 SER A 125 REMARK 465 VAL A 126 REMARK 465 ASP A 127 REMARK 465 VAL A 251 REMARK 465 PRO A 252 REMARK 465 ARG A 253 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 THR A 52 -44.82 67.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 6LFV A 1 253 PDB 6LFV 6LFV 1 253 SEQRES 1 A 253 MET ASP ILE GLN MET THR GLN THR ALA SER SER LEU SER SEQRES 2 A 253 ALA SER LEU GLY ASP ARG VAL THR ILE SER CYS ARG ALA SEQRES 3 A 253 SER GLN TYR ILE ASN ASN TYR LEU ASN TRP TYR GLN GLN SEQRES 4 A 253 LYS PRO ASP GLY THR VAL THR LEU LEU ILE TYR TYR THR SEQRES 5 A 253 SER ILE LEU HIS SER GLY VAL PRO SER ARG PHE ILE GLY SEQRES 6 A 253 SER GLY SER GLY THR ASP TYR SER LEU THR ILE SER ASN SEQRES 7 A 253 LEU ASP GLN GLU ASP ILE ALA THR TYR PHE CYS GLN GLN SEQRES 8 A 253 GLY TYR THR LEU PRO LEU THR PHE GLY ALA GLY THR LYS SEQRES 9 A 253 LEU GLU LEU LYS ARG PRO GLY GLY GLY GLY SER GLY GLY SEQRES 10 A 253 GLY GLY SER GLY GLY GLY GLY SER VAL ASP GLU VAL LYS SEQRES 11 A 253 LEU VAL GLU SER GLY GLY GLY LEU VAL LYS PRO GLY GLY SEQRES 12 A 253 SER LEU LYS LEU SER CYS ALA ALA SER GLY PHE THR PHE SEQRES 13 A 253 SER THR TYR GLY MET SER TRP VAL ARG GLN THR PRO GLU SEQRES 14 A 253 LYS ARG LEU GLU TRP VAL ALA SER ILE SER GLY GLY GLY SEQRES 15 A 253 ASP THR TYR TYR THR ASP ILE VAL LYS GLY ARG VAL THR SEQRES 16 A 253 ILE SER ARG ASP ASN ASP ARG ASN ILE LEU TYR LEU GLN SEQRES 17 A 253 MET SER SER LEU ARG SER GLU ASP THR ALA MET TYR HIS SEQRES 18 A 253 CYS THR ARG GLY ALA LEU VAL ARG LEU PRO HIS TYR TYR SEQRES 19 A 253 SER MET ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SEQRES 20 A 253 SER SER LEU VAL PRO ARG FORMUL 2 HOH *107(H2 O) HELIX 1 AA1 ASP A 80 ILE A 84 5 5 HELIX 2 AA2 THR A 155 TYR A 159 5 5 HELIX 3 AA3 ASP A 188 LYS A 191 5 4 HELIX 4 AA4 ARG A 213 THR A 217 5 5 SHEET 1 AA1 4 MET A 5 THR A 6 0 SHEET 2 AA1 4 VAL A 20 ALA A 26 -1 O ARG A 25 N THR A 6 SHEET 3 AA1 4 ASP A 71 ILE A 76 -1 O LEU A 74 N ILE A 22 SHEET 4 AA1 4 PHE A 63 SER A 68 -1 N ILE A 64 O THR A 75 SHEET 1 AA2 6 SER A 11 ALA A 14 0 SHEET 2 AA2 6 THR A 103 LEU A 107 1 O GLU A 106 N LEU A 12 SHEET 3 AA2 6 THR A 86 GLN A 91 -1 N TYR A 87 O THR A 103 SHEET 4 AA2 6 LEU A 34 GLN A 39 -1 N GLN A 39 O THR A 86 SHEET 5 AA2 6 VAL A 45 TYR A 50 -1 O ILE A 49 N TRP A 36 SHEET 6 AA2 6 ILE A 54 LEU A 55 -1 O ILE A 54 N TYR A 50 SHEET 1 AA3 4 SER A 11 ALA A 14 0 SHEET 2 AA3 4 THR A 103 LEU A 107 1 O GLU A 106 N LEU A 12 SHEET 3 AA3 4 THR A 86 GLN A 91 -1 N TYR A 87 O THR A 103 SHEET 4 AA3 4 THR A 98 PHE A 99 -1 O THR A 98 N GLN A 91 SHEET 1 AA4 4 LYS A 130 SER A 134 0 SHEET 2 AA4 4 LEU A 145 SER A 152 -1 O SER A 148 N SER A 134 SHEET 3 AA4 4 ILE A 204 MET A 209 -1 O MET A 209 N LEU A 145 SHEET 4 AA4 4 VAL A 194 ASP A 199 -1 N SER A 197 O TYR A 206 SHEET 1 AA5 6 GLY A 137 VAL A 139 0 SHEET 2 AA5 6 THR A 243 VAL A 247 1 O THR A 246 N GLY A 137 SHEET 3 AA5 6 ALA A 218 ARG A 229 -1 N TYR A 220 O THR A 243 SHEET 4 AA5 6 GLY A 160 GLN A 166 -1 N VAL A 164 O HIS A 221 SHEET 5 AA5 6 LEU A 172 ILE A 178 -1 O GLU A 173 N ARG A 165 SHEET 6 AA5 6 THR A 184 TYR A 186 -1 O TYR A 185 N SER A 177 SHEET 1 AA6 4 GLY A 137 VAL A 139 0 SHEET 2 AA6 4 THR A 243 VAL A 247 1 O THR A 246 N GLY A 137 SHEET 3 AA6 4 ALA A 218 ARG A 229 -1 N TYR A 220 O THR A 243 SHEET 4 AA6 4 TYR A 233 TRP A 239 -1 O TYR A 233 N VAL A 228 SSBOND 1 CYS A 24 CYS A 89 1555 1555 2.03 SSBOND 2 CYS A 149 CYS A 222 1555 1555 2.04 CISPEP 1 LEU A 95 PRO A 96 0 -1.26 CISPEP 2 LEU A 230 PRO A 231 0 0.80 CRYST1 92.420 92.420 53.830 90.00 90.00 90.00 I 4 8 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 0.010820 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018577 0.00000