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HEADER IMMUNOGLOBULIN 01-NOV-93 1FGV TITLE X-RAY STRUCTURES OF FRAGMENTS FROM BINDING AND NONBINDING TITLE 2 VERSIONS OF A HUMANIZED ANTI-CD18 ANTIBODY: STRUCTURAL TITLE 3 INDICATIONS OF THE KEY ROLE OF VH RESIDUES 59 TO 65 COMPND MOL_ID: 1; COMPND 2 MOLECULE: H52 FV (LIGHT CHAIN); COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: H52 FV (HEAVY CHAIN); COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2 KEYWDS IMMUNOGLOBULIN EXPDTA X-RAY DIFFRACTION AUTHOR C.EIGENBROT,J.KESSLER REVDAT 1 31-JAN-94 1FGV 0 JRNL AUTH C.EIGENBROT,T.GONZALEZ,J.MAYEDA,P.CARTER,W.WERTHER, JRNL AUTH 2 T.HOTALING,J.FOX,J.KESSLER JRNL TITL X-RAY STRUCTURES OF FRAGMENTS FROM BINDING AND JRNL TITL 2 NONBINDING VERSIONS OF A HUMANIZED ANTI-CD18 JRNL TITL 3 ANTIBODY: STRUCTURAL INDICATIONS OF THE KEY ROLE JRNL TITL 4 OF VH RESIDUES 59 TO 65. JRNL REF PROTEINS V. 18 49 1994 JRNL REFN ASTM PSFGEY US ISSN 0887-3585 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1743 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 2.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FGV COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 32.10000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.10000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.65000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: L, H 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 720 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 ARG L 108 REMARK 465 THR L 109 REMARK 465 ASN H 103 REMARK 465 TYR H 104 REMARK 465 GLY H 105 REMARK 465 PHE H 106 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS L 107 CG CD CE NZ REMARK 470 GLU H 1 CG CD OE1 OE2 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL H 108 N - CA - CB ANGL. DEV. =-18.4 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 THR L 51 -48.71 67.33 DBREF 1FGV L 1 107 GB 259596 AAB24132 1 107 SEQADV 1FGV ASN L 30 GB 259596 ARG 30 CONFLICT SEQADV 1FGV THR L 53 GB 259596 ARG 53 CONFLICT SEQADV 1FGV PRO L 96 GB 259596 TRP 96 CONFLICT SEQADV 1FGV ALA L 100 GB 259596 GLN 100 CONFLICT SEQRES 1 L 109 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 109 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 109 GLN ASP ILE ASN ASN TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 L 109 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR TYR THR SER SEQRES 5 L 109 THR LEU GLU SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 109 GLY SER GLY THR ASP TYR THR LEU THR ILE SER SER LEU SEQRES 7 L 109 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN GLY SEQRES 8 L 109 ASN THR LEU PRO PRO THR PHE GLY ALA GLY THR LYS VAL SEQRES 9 L 109 GLU ILE LYS ARG THR SEQRES 1 H 124 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 124 PRO GLY GLY SER LEU ARG LEU SER CYS ALA THR SER GLY SEQRES 3 H 124 TYR THR PHE THR GLU TYR THR MET HIS TRP MET ARG GLN SEQRES 4 H 124 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA GLY ILE ASN SEQRES 5 H 124 PRO LYS ASN GLY GLY THR SER TYR ALA ASP SER VAL LYS SEQRES 6 H 124 GLY ARG PHE THR ILE SER VAL ASP LYS SER LYS ASN THR SEQRES 7 H 124 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 124 ALA VAL TYR TYR CYS ALA ARG TRP ARG GLY LEU ASN TYR SEQRES 9 H 124 GLY PHE ASP VAL ARG TYR PHE ASP VAL TRP GLY GLN GLY SEQRES 10 H 124 THR LEU VAL THR VAL SER SER FTNOTE 1 CIS PROLINE - PRO L 8 FTNOTE 2 CIS PROLINE - PRO L 95 FORMUL 3 HOH *109(H2 O) HELIX 1 A1 PRO L 80 ASP L 82 5 3 HELIX 2 A2 PHE H 29 GLU H 31 5 3 HELIX 3 A3 ALA H 88 ASP H 90 5 3 SHEET 1 A1 4 MET L 4 SER L 7 0 SHEET 2 A1 4 VAL L 19 ARG L 24 -1 N THR L 22 O SER L 7 SHEET 3 A1 4 ASP L 70 ILE L 75 -1 N LEU L 73 O ILE L 21 SHEET 4 A1 4 PHE L 62 SER L 67 -1 O SER L 63 N THR L 74 SHEET 1 A2 6 SER L 10 ALA L 13 0 SHEET 2 A2 6 THR L 97 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 A2 6 THR L 85 GLN L 90 -1 O CYS L 88 N GLY L 99 SHEET 4 A2 6 LEU L 33 GLN L 38 -1 O GLN L 38 N THR L 85 SHEET 5 A2 6 LYS L 45 TYR L 49 -1 N LYS L 45 O GLN L 37 SHEET 6 A2 6 THR L 53 LEU L 54 -1 O THR L 53 N TYR L 49 SHEET 1 B1 4 GLN H 3 SER H 7 0 SHEET 2 B1 4 LEU H 18 SER H 25 -1 N SER H 21 O SER H 7 SHEET 3 B1 4 THR H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 B1 4 PHE H 68 ASP H 73 -1 O SER H 71 N TYR H 80 SHEET 1 B2 6 GLY H 10 VAL H 12 0 SHEET 2 B2 6 TYR H 110 VAL H 122 1 O LEU H 119 N GLY H 10 SHEET 3 B2 6 ALA H 92 ARG H 100 -1 O ALA H 92 N VAL H 120 SHEET 4 B2 6 MET H 34 GLN H 39 -1 O GLN H 39 N VAL H 93 SHEET 5 B2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 B2 6 THR H 58 TYR H 60 -1 N SER H 59 O GLY H 50 TURN 1 T1 SER L 14 ASP L 17 TURN 2 T2 ILE L 29 TYR L 32 TURN 3 T3 LYS L 39 LYS L 42 TURN 4 T4 TYR L 49 THR L 53 I+4 TURN 5 T5 GLU L 55 VAL L 58 TURN 6 T6 PRO L 59 PHE L 62 TURN 7 T7 SER L 67 ASP L 70 TURN 8 T8 GLN H 13 GLY H 16 TURN 9 T9 ALA H 40 LYS H 43 TURN 10 T10 ASN H 52 GLY H 56 I+4 TURN 11 T11 ALA H 61 VAL H 64 TURN 12 T12 LYS H 65 PHE H 68 TURN 13 T13 ASP H 73 THR H 78 I+5 SSBOND 1 CYS L 23 CYS L 88 SSBOND 2 CYS H 22 CYS H 96 CISPEP 1 SER L 7 PRO L 8 0 -5.61 CISPEP 2 LEU L 94 PRO L 95 0 -0.33 CRYST1 64.200 61.300 51.800 90.00 99.00 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 0.015576 0.000000 0.002467 0.00000 SCALE2 0.000000 0.016313 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019546 0.00000