10 20 30 40 50 60 70 80 1A2J - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 06-JAN-98 1A2J
TITLE OXIDIZED DSBA CRYSTAL FORM II
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISULFIDE BOND FORMATION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DSBA
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELLULAR_LOCATION: PERIPLASM
KEYWDS OXIDOREDUCTASE, PROTEIN DISULFIDE ISOMERASE, PROTEIN KEYWDS 2 FOLDING, REDOX PROTEIN, REDOX-ACTIVE CENTER
EXPDTA X-RAY DIFFRACTION
AUTHOR J.L.MARTIN,L.W.GUDDAT
REVDAT 2 24-FEB-09 1A2J 1 VERSN REVDAT 1 16-SEP-98 1A2J 0
JRNL AUTH L.W.GUDDAT,J.C.BARDWELL,J.L.MARTIN JRNL TITL CRYSTAL STRUCTURES OF REDUCED AND OXIDIZED DSBA: JRNL TITL 2 INVESTIGATION OF DOMAIN MOTION AND THIOLATE JRNL TITL 3 STABILIZATION. JRNL REF STRUCTURE V. 6 757 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9655827 JRNL DOI 10.1016/S0969-2126(98)00077-X
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.W.GUDDAT,J.C.BARDWELL,T.ZANDER,J.L.MARTIN REMARK 1 TITL THE UNCHARGED SURFACE FEATURES SURROUNDING THE REMARK 1 TITL 2 ACTIVE SITE OF ESCHERICHIA COLI DSBA ARE CONSERVED REMARK 1 TITL 3 AND ARE IMPLICATED IN PEPTIDE BINDING REMARK 1 REF PROTEIN SCI. V. 6 1148 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.W.GUDDAT,J.C.BARDWELL,R.GLOCKSHUBER, REMARK 1 AUTH 2 M.HUBER-WUNDERLICH,T.ZANDER,J.L.MARTIN REMARK 1 TITL STRUCTURAL ANALYSIS OF THREE HIS32 MUTANTS OF REMARK 1 TITL 2 DSBA: SUPPORT FOR AN ELECTROSTATIC ROLE OF HIS32 REMARK 1 TITL 3 IN DSBA STABILITY REMARK 1 REF PROTEIN SCI. V. 6 1893 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.L.MARTIN,J.C.BARDWELL,J.KURIYAN REMARK 1 TITL CRYSTAL STRUCTURE OF THE DSBA PROTEIN REQUIRED FOR REMARK 1 TITL 2 DISULPHIDE BOND FORMATION IN VIVO REMARK 1 REF NATURE V. 365 464 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH J.L.MARTIN,G.WAKSMAN,J.C.BARDWELL,J.BECKWITH, REMARK 1 AUTH 2 J.KURIYAN REMARK 1 TITL CRYSTALLIZATION OF DSBA, AN ESCHERICHIA COLI REMARK 1 TITL 2 PROTEIN REQUIRED FOR DISULPHIDE BOND FORMATION IN REMARK 1 TITL 3 VIVO REMARK 1 REF J.MOL.BIOL. V. 230 1097 1993 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 10332 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) : 0.182 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1069 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 963 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.16 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 126 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 : 1446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 50.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.96 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 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EIGHT RESIDUES GLU 4, GLU 13, LYS REMARK 3 48, LYS 98, GLU 120, LYS 132, GLN 146, AND LYS 183 WERE REMARK 3 MODELLED AS ALANINE BECAUSE OF POORLY DEFINED SIDE CHAIN REMARK 3 DENSITY. RESIDUES GLU 85, SER 106, SER 133, AND SER 186 WERE REMARK 3 MODELLED WITH TWO ALTERNATE CONFORMATIONS, EACH OF HALF REMARK 3 OCCUPANCY. THE SIDE CHAINS OF GLU 13, GLU 85, SER 106, SER REMARK 3 133, AND SER 186 WERE MODELLED WITH TWO ALTERNATE REMARK 3 CONFORMATIONS, EACH OF HALF OCCUPANCY.
REMARK 4 REMARK 4 1A2J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-95 REMARK 200 TEMPERATURE (KELVIN) : 289 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38303 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15300 REMARK 200 R SYM FOR SHELL (I) : 0.15300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1FVK REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 4K IN 0.1M ACETATE BUFFER REMARK 280 PH 5.0
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.69000 REMARK 290 SMTRY3 2 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 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 LYS A 189
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 GLU A 4 CG CD OE1 OE2 REMARK 470 GLU A 13 CG CD OE1 OE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 GLU A 120 CG CD OE1 OE2 REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 LYS A 183 CG CD CE NZ
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 LYS A 7 -87.20 -87.98 REMARK 500 PHE A 29 41.63 -100.96 REMARK 500 VAL A 39 -69.89 -91.01 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: THE ACTIVE SITE.
DBREF 1A2J A 1 189 UNP P24991 DSBA_ECOLI 20 208
SEQRES 1 A 189 ALA GLN TYR GLU ASP GLY LYS GLN TYR THR THR LEU GLU SEQRES 2 A 189 LYS PRO VAL ALA GLY ALA PRO GLN VAL LEU GLU PHE PHE SEQRES 3 A 189 SER PHE PHE CYS PRO HIS CYS TYR GLN PHE GLU GLU VAL SEQRES 4 A 189 LEU HIS ILE SER ASP ASN VAL LYS LYS LYS LEU PRO GLU SEQRES 5 A 189 GLY VAL LYS MET THR LYS TYR HIS VAL ASN PHE MET GLY SEQRES 6 A 189 GLY ASP LEU GLY LYS ASP LEU THR GLN ALA TRP ALA VAL SEQRES 7 A 189 ALA MET ALA LEU GLY VAL GLU ASP LYS VAL THR VAL PRO SEQRES 8 A 189 LEU PHE GLU GLY VAL GLN LYS THR GLN THR ILE ARG SER SEQRES 9 A 189 ALA SER ASP ILE ARG ASP VAL PHE ILE ASN ALA GLY ILE SEQRES 10 A 189 LYS GLY GLU GLU TYR ASP ALA ALA TRP ASN SER PHE VAL SEQRES 11 A 189 VAL LYS SER LEU VAL ALA GLN GLN GLU LYS ALA ALA ALA SEQRES 12 A 189 ASP VAL GLN LEU ARG GLY VAL PRO ALA MET PHE VAL ASN SEQRES 13 A 189 GLY LYS TYR GLN LEU ASN PRO GLN GLY MET ASP THR SER SEQRES 14 A 189 ASN MET ASP VAL PHE VAL GLN GLN TYR ALA ASP THR VAL SEQRES 15 A 189 LYS TYR LEU SER GLU LYS LYS
FORMUL 2 HOH *90(H2 O)
HELIX 1 H1 PRO A 31 GLU A 38 1 8 HELIX 2 H2 ILE A 42 LYS A 49 1 8 HELIX 3 H3 GLY A 66 LEU A 82 1 17 HELIX 4 H4 GLU A 85 GLN A 97 1 13 HELIX 5 H5 ALA A 105 ASN A 114 1 10 HELIX 6 H6 GLY A 119 ASN A 127 1 9 HELIX 7 H7 PHE A 129 ASP A 144 1 16 HELIX 8 H8 PRO A 163 GLY A 165 1 3 HELIX 9 H9 MET A 171 SER A 186 1 16
SHEET 1 S1 1 TYR A 9 THR A 11 0
SSBOND 1 CYS A 30 CYS A 33 1555 1555 2.03
CISPEP 1 VAL A 150 PRO A 151 0 0.19
SITE 1 CAA 4 CYS A 30 PRO A 31 HIS A 32 CYS A 33
CRYST1 38.520 51.380 42.500 90.00 103.08 90.00 P 1 21 1 2
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 0.025961 0.000000 0.006032 0.00000
SCALE2 0.000000 0.019463 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024156 0.00000