HEADER IMMUNOGLOBULIN/HYDROLASE(O-GLYCOSYL) 03-DEC-93 1VFB TITLE BOUND WATER MOLECULES AND CONFORMATIONAL STABILIZATION HELP TITLE 2 MEDIATE AN ANTIGEN-ANTIBODY ASSOCIATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: IGG1-KAPPA D1.3 FV (LIGHT CHAIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: IGG1-KAPPA D1.3 FV (HEAVY CHAIN); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HEN EGG WHITE LYSOZYME; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGAN: EGG; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 7 ORGAN: EGG; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: GALLUS GALLUS KEYWDS IMMUNOGLOBULIN/HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR T.N.BHAT,R.J.POLJAK REVDAT 2 01-APR-03 1VFB 1 JRNL REVDAT 1 31-MAY-94 1VFB 0 JRNL AUTH T.N.BHAT,G.A.BENTLEY,G.BOULOT,M.I.GREENE,D.TELLO, JRNL AUTH 2 W.DALL'ACQUA,H.SOUCHON,F.P.SCHWARZ,R.A.MARIUZZA, JRNL AUTH 3 R.J.POLJAK JRNL TITL BOUND WATER MOLECULES AND CONFORMATIONAL JRNL TITL 2 STABILIZATION HELP MEDIATE AN ANTIGEN-ANTIBODY JRNL TITL 3 ASSOCIATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 91 1089 1994 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.N.BHAT,G.A.BENTLEY,T.O.FISCHMANN,G.BOULOT, REMARK 1 AUTH 2 R.J.POLJAK REMARK 1 TITL SMALL REARRANGEMENTS IN STRUCTURES OF FV AND FAB REMARK 1 TITL 2 FRAGMENTS OF AN ANTIBODY D1.3 ON ANTIGEN BINDING REMARK 1 REF NATURE V. 347 483 1990 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : NULL 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) : 0.185 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 : 3408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 48 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.70 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 1VFB 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 (%): 50.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 64.60000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.60000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.40000 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 3 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: A, B, 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 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 A 51 -39.97 65.50 DBREF 1VFB A 1 107 GB 545862 AAB30177 1 108 DBREF 1VFB B 1 116 GB 896294 AAA69766 133 248 DBREF 1VFB C 1 129 UNP P00698 LYSC_CHICK 19 147 SEQADV 1VFB VAL A 3 GB 545862 GLU 3 CONFLICT SEQADV 1VFB TYR A 50 GB 545862 LYS 50 CONFLICT SEQADV 1VFB THR A 51 GB 545862 ALA 51 CONFLICT SEQADV 1VFB THR A 52 GB 545862 GLN 52 CONFLICT SEQADV 1VFB A GB 545862 PRO 95 DELETION SEQADV 1VFB ARG A 96 GB 545862 TRP 97 CONFLICT SEQADV 1VFB LEU B 112 GB 896294 VAL 244 CONFLICT SEQRES 1 A 107 ASP ILE VAL LEU THR GLN SER PRO ALA SER LEU SER ALA SEQRES 2 A 107 SER VAL GLY GLU THR VAL THR ILE THR CYS ARG ALA SER SEQRES 3 A 107 GLY ASN ILE HIS ASN TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 A 107 GLN GLY LYS SER PRO GLN LEU LEU VAL TYR TYR THR THR SEQRES 5 A 107 THR LEU ALA ASP GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 A 107 GLY SER GLY THR GLN TYR SER LEU LYS ILE ASN SER LEU SEQRES 7 A 107 GLN PRO GLU ASP PHE GLY SER TYR TYR CYS GLN HIS PHE SEQRES 8 A 107 TRP SER THR PRO ARG THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 A 107 GLU ILE LYS SEQRES 1 B 116 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL ALA SEQRES 2 B 116 PRO SER GLN SER LEU SER ILE THR CYS THR VAL SER GLY SEQRES 3 B 116 PHE SER LEU THR GLY TYR GLY VAL ASN TRP VAL ARG GLN SEQRES 4 B 116 PRO PRO GLY LYS GLY LEU GLU TRP LEU GLY MET ILE TRP SEQRES 5 B 116 GLY ASP GLY ASN THR ASP TYR ASN SER ALA LEU LYS SER SEQRES 6 B 116 ARG LEU SER ILE SER LYS ASP ASN SER LYS SER GLN VAL SEQRES 7 B 116 PHE LEU LYS MET ASN SER LEU HIS THR ASP ASP THR ALA SEQRES 8 B 116 ARG TYR TYR CYS ALA ARG GLU ARG ASP TYR ARG LEU ASP SEQRES 9 B 116 TYR TRP GLY GLN GLY THR THR LEU THR VAL SER SER SEQRES 1 C 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 C 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 C 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 C 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 C 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 C 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 C 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 C 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 C 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 C 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU FTNOTE 1 CIS PROLINE - PRO A 8 FTNOTE 2 CIS PROLINE - PRO A 95 FORMUL 4 HOH *48(H2 O) HELIX 1 1 GLN A 79 PHE A 83 5 5 HELIX 2 2 LEU B 63 SER B 65 5 3 HELIX 3 3 HIS B 86 THR B 90 5 5 HELIX 4 4 GLY C 4 HIS C 15 1 12 HELIX 5 5 SER C 24 ASN C 37 1 14 HELIX 6 6 CYS C 80 SER C 85 5 6 HELIX 7 7 ILE C 88 VAL C 99 1 12 HELIX 8 8 ASN C 103 ALA C 107 5 5 HELIX 9 9 TRP C 108 CYS C 115 1 8 HELIX 10 10 ASP C 119 ILE C 124 5 6 SHEET 1 A 4 LEU A 4 SER A 7 0 SHEET 2 A 4 VAL A 19 ALA A 25 -1 N THR A 22 O SER A 7 SHEET 3 A 4 GLN A 70 ILE A 75 -1 O TYR A 71 N CYS A 23 SHEET 4 A 4 PHE A 62 SER A 67 -1 O SER A 63 N LYS A 74 SHEET 1 B 6 SER A 10 ALA A 13 0 SHEET 2 B 6 THR A 102 ILE A 106 1 O LYS A 103 N LEU A 11 SHEET 3 B 6 GLY A 84 HIS A 90 -1 O GLY A 84 N LEU A 104 SHEET 4 B 6 LEU A 33 GLN A 38 -1 N ALA A 34 O GLN A 89 SHEET 5 B 6 GLN A 45 TYR A 49 -1 O GLN A 45 N GLN A 37 SHEET 6 B 6 THR A 53 LEU A 54 -1 O THR A 53 N TYR A 49 SHEET 1 C 4 GLN B 3 SER B 7 0 SHEET 2 C 4 LEU B 18 SER B 25 -1 N THR B 21 O SER B 7 SHEET 3 C 4 GLN B 77 MET B 82 -1 O VAL B 78 N CYS B 22 SHEET 4 C 4 LEU B 67 ASP B 72 -1 O SER B 68 N LYS B 81 SHEET 1 D 5 THR B 57 TYR B 59 0 SHEET 2 D 5 GLU B 46 ILE B 51 -1 N MET B 50 O ASP B 58 SHEET 3 D 5 GLY B 33 GLN B 39 -1 N VAL B 34 O ILE B 51 SHEET 4 D 5 ALA B 91 GLU B 98 -1 O ARG B 92 N GLN B 39 SHEET 5 D 5 LEU B 103 TRP B 106 -1 N ASP B 104 O ARG B 97 SHEET 1 E 6 THR B 57 TYR B 59 0 SHEET 2 E 6 GLU B 46 ILE B 51 -1 N MET B 50 O ASP B 58 SHEET 3 E 6 GLY B 33 GLN B 39 -1 N VAL B 34 O ILE B 51 SHEET 4 E 6 ALA B 91 GLU B 98 -1 O ARG B 92 N GLN B 39 SHEET 5 E 6 THR B 110 VAL B 114 -1 O THR B 110 N TYR B 93 SHEET 6 E 6 LEU B 11 VAL B 12 1 N VAL B 12 O THR B 113 SHEET 1 F 3 THR C 43 ARG C 45 0 SHEET 2 F 3 THR C 51 TYR C 53 -1 N ASP C 52 O ASN C 44 SHEET 3 F 3 ILE C 58 ASN C 59 -1 O ILE C 58 N TYR C 53 SSBOND 1 CYS A 23 CYS A 88 SSBOND 2 CYS B 22 CYS B 95 SSBOND 3 CYS C 6 CYS C 127 SSBOND 4 CYS C 30 CYS C 115 SSBOND 5 CYS C 64 CYS C 80 SSBOND 6 CYS C 76 CYS C 94 CISPEP 1 SER A 7 PRO A 8 0 -2.16 CISPEP 2 THR A 94 PRO A 95 0 -4.58 CRYST1 129.200 60.800 56.900 90.00 119.30 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 0.007740 0.000000 0.004343 0.00000 SCALE2 0.000000 0.016447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020153 0.00000