HEADER OXIDOREDUCTASE 16-SEP-96 1BED TITLE STRUCTURE OF DISULFIDE OXIDOREDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DSBA OXIDOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TCPG, DISULFIDE BOND FORMATION PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666 KEYWDS TCPG, PROTEIN DISULFIDE ISOMERASE, DISULFIDE OXIDOREDUCTASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.-H.HU,J.L.MARTIN REVDAT 3 02-AUG-23 1BED 1 SEQADV REVDAT 2 24-FEB-09 1BED 1 VERSN REVDAT 1 08-OCT-97 1BED 0 JRNL AUTH S.H.HU,J.A.PEEK,E.RATTIGAN,R.K.TAYLOR,J.L.MARTIN JRNL TITL STRUCTURE OF TCPG, THE DSBA PROTEIN FOLDING CATALYST FROM JRNL TITL 2 VIBRIO CHOLERAE. JRNL REF J.MOL.BIOL. V. 268 137 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9149147 JRNL DOI 10.1006/JMBI.1997.0940 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.PEEK,R.K.TAYLOR REMARK 1 TITL CHARACTERIZATION OF A PERIPLASMIC THIOL:DISULFIDE REMARK 1 TITL 2 INTERCHANGE PROTEIN REQUIRED FOR THE FUNCTIONAL MATURATION REMARK 1 TITL 3 OF SECRETED VIRULENCE FACTORS OF VIBRIO CHOLERAE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 6210 1992 REMARK 1 REFN ISSN 0027-8424 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) : 20.00 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) (%) : 70.0 REMARK 3 NUMBER OF REFLECTIONS : 9309 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 931 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 681 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 75 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 : 1374 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.20 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 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 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171655. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-94 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 6.0-6.5 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12974 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 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 (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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 1DSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-13% EG 4K, 0.1M MES, PH 6.0-6.5, PH REMARK 280 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 32.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 32.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.40000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.75000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.40000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.75000 REMARK 290 SMTRY3 8 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 97.20000 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 A 4 CG CD CE NZ REMARK 470 GLN A 10 CG CD OE1 NE2 REMARK 470 VAL A 11 CG1 CG2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 SER A 18 OG REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 GLN A 46 CG CD OE1 NE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 GLN A 160 CG CD OE1 NE2 REMARK 470 GLN A 162 CG CD OE1 NE2 REMARK 470 VAL A 164 CG1 CG2 REMARK 470 LYS A 165 CG CD CE NZ REMARK 470 SER A 166 OG REMARK 470 LEU A 167 CG CD1 CD2 REMARK 470 ASP A 168 CG OD1 OD2 REMARK 470 TYR A 176 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 181 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 GLU A 7 -54.56 -131.51 REMARK 500 HIS A 94 -60.01 -97.73 REMARK 500 ASN A 155 -5.62 70.07 REMARK 500 GLN A 160 52.72 -91.75 REMARK 500 GLN A 162 2.00 -62.21 REMARK 500 LYS A 165 -91.68 -71.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BED A 1 181 UNP P32557 DSBA_VIBCH 20 200 SEQADV 1BED SER A 23 UNP P32557 ASN 42 CONFLICT SEQRES 1 A 181 ALA GLN PHE LYS GLU GLY GLU HIS TYR GLN VAL LEU LYS SEQRES 2 A 181 THR PRO ALA SER SER SER PRO VAL VAL SER GLU PHE PHE SEQRES 3 A 181 SER PHE TYR CYS PRO HIS CYS ASN THR PHE GLU PRO ILE SEQRES 4 A 181 ILE ALA GLN LEU LYS GLN GLN LEU PRO GLU GLY ALA LYS SEQRES 5 A 181 PHE GLN LYS ASN HIS VAL SER PHE MET GLY GLY ASN MET SEQRES 6 A 181 GLY GLN ALA MET SER LYS ALA TYR ALA THR MET ILE ALA SEQRES 7 A 181 LEU GLU VAL GLU ASP LYS MET VAL PRO VAL MET PHE ASN SEQRES 8 A 181 ARG ILE HIS THR LEU ARG LYS PRO PRO LYS ASP GLU GLN SEQRES 9 A 181 GLU LEU ARG GLN ILE PHE LEU ASP GLU GLY ILE ASP ALA SEQRES 10 A 181 ALA LYS PHE ASP ALA ALA TYR ASN GLY PHE ALA VAL ASP SEQRES 11 A 181 SER MET VAL ARG ARG PHE ASP LYS GLN PHE GLN ASP SER SEQRES 12 A 181 GLY LEU THR GLY VAL PRO ALA VAL VAL VAL ASN ASN ARG SEQRES 13 A 181 TYR LEU VAL GLN GLY GLN SER VAL LYS SER LEU ASP GLU SEQRES 14 A 181 TYR PHE ASP LEU VAL ASN TYR LEU LEU THR LEU LYS FORMUL 2 HOH *53(H2 O) HELIX 1 1 CYS A 30 GLU A 37 1 8 HELIX 2 1' PRO A 38 LEU A 47 1 10 HELIX 3 2 GLY A 63 LEU A 79 1 17 HELIX 4 3 VAL A 81 HIS A 94 1 14 HELIX 5 4 ASP A 102 GLU A 113 1 12 HELIX 6 5 ASP A 116 ASN A 125 1 10 HELIX 7 6 PHE A 127 GLY A 144 1 18 HELIX 8 7 SER A 166 THR A 179 1 14 SHEET 1 A 2 HIS A 8 LEU A 12 0 SHEET 2 A 2 ARG A 156 GLN A 160 -1 N LEU A 158 O GLN A 10 SHEET 1 B 3 LYS A 52 VAL A 58 0 SHEET 2 B 3 VAL A 21 PHE A 26 1 N VAL A 22 O LYS A 52 SHEET 3 B 3 ALA A 150 ASN A 154 -1 N VAL A 152 O SER A 23 SSBOND 1 CYS A 30 CYS A 33 1555 1555 2.04 CISPEP 1 VAL A 148 PRO A 149 0 -0.44 CRYST1 64.000 91.500 64.800 90.00 90.00 90.00 C 2 2 21 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 0.015625 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015432 0.00000