HEADER STRUCTURAL GENOMICS 21-MAR-14 4PWP TITLE CRYSTAL STRUCTURE OF DSBA FROM THE GRAM POSITIVE BACTERIUM TITLE 2 CORYNEBACTERIUM DIPHTHERIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DSBA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THIOREDOXIN DOMAIN, DISULFIDE BOND ISOMERASE, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR S.H.UM,J.S.KIM,L.JIAO,B.Y.YOON,I.JO,N.C.HA REVDAT 1 25-MAR-15 4PWP 0 JRNL AUTH S.H.UM,J.S.KIM,L.JIAO,B.Y.YOON,I.JO,N.C.HA JRNL TITL CRYSTAL STRUCTURE AND BIOCHEMICAL CHARACTERIZATION OF DSBA JRNL TITL 2 FROM THE GRAM POSITIVE BACTERIUM CORYNEBACTERIUM DIPHTHERIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21892 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 30.8607 - 4.3427 0.98 1521 149 0.1487 0.1862 REMARK 3 2 4.3427 - 3.4484 1.00 1460 146 0.1394 0.1775 REMARK 3 3 3.4484 - 3.0129 1.00 1450 144 0.1743 0.2065 REMARK 3 4 3.0129 - 2.7376 1.00 1427 140 0.1821 0.2136 REMARK 3 5 2.7376 - 2.5415 1.00 1421 148 0.1917 0.2333 REMARK 3 6 2.5415 - 2.3917 1.00 1425 141 0.1759 0.2253 REMARK 3 7 2.3917 - 2.2720 1.00 1415 139 0.1731 0.2350 REMARK 3 8 2.2720 - 2.1731 1.00 1411 142 0.1660 0.1843 REMARK 3 9 2.1731 - 2.0895 1.00 1404 139 0.1623 0.1955 REMARK 3 10 2.0895 - 2.0174 1.00 1407 138 0.1649 0.2103 REMARK 3 11 2.0174 - 1.9543 1.00 1391 139 0.1569 0.2014 REMARK 3 12 1.9543 - 1.8984 1.00 1417 143 0.1617 0.2273 REMARK 3 13 1.8984 - 1.8485 1.00 1390 146 0.1535 0.2249 REMARK 3 14 1.8485 - 1.8030 0.98 1363 136 0.1595 0.2049 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.980 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 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 : 0.006 2103 REMARK 3 ANGLE : 1.056 2876 REMARK 3 CHIRALITY : 0.043 307 REMARK 3 PLANARITY : 0.005 394 REMARK 3 DIHEDRAL : 13.568 799 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 4PWP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-14. REMARK 100 THE RCSB ID CODE IS RCSB085313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40982 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 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 (%) : 99.7 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: COOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 2K, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.40950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.56950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.21750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.56950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.40950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.21750 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 231 O HOH A 581 2.11 REMARK 500 OD2 ASP A 113 O HOH A 591 2.11 REMARK 500 OE2 GLU A 231 O HOH A 582 2.16 REMARK 500 O HOH A 518 O HOH A 595 2.17 REMARK 500 O HOH A 569 O HOH A 570 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 610 O HOH A 613 4466 2.04 REMARK 500 O HOH A 598 O HOH A 609 3646 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 39 51.57 -91.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PWO RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT REMARK 999 KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THIS REMARK 999 SEQUENCE HAS A GENEBANK ACCESSION NUMBER, CAE48901.1. DBREF 4PWP A 38 287 PDB 4PWP 4PWP 38 287 SEQRES 1 A 250 THR GLN ALA GLU LYS THR ALA THR ASP LEU PRO PRO GLY SEQRES 2 A 250 PHE SER GLY LYS ALA GLY SER VAL ASN ALA THR PRO GLY SEQRES 3 A 250 THR LYS GLY LEU ASP GLY PRO THR PRO LEU ALA ASP GLY SEQRES 4 A 250 SER PHE ASP ALA THR ILE PHE GLY PRO ALA LYS GLU LEU SEQRES 5 A 250 LYS SER ALA ASP ASP ILE LEU ASN VAL HIS ARG ARG ASN SEQRES 6 A 250 ALA LYS ASP PRO PHE ALA VAL GLY SER VAL ASP ALA PRO SEQRES 7 A 250 LEU VAL ILE THR GLU PHE SER ASP PHE GLU CYS PRO PHE SEQRES 8 A 250 CYS ALA ARG TRP SER ASN GLN THR GLU PRO MSE LEU MSE SEQRES 9 A 250 GLU GLU TYR VAL SER LYS GLY LEU VAL ARG ILE GLU TRP SEQRES 10 A 250 ASN ASP LEU PRO VAL ASN GLY GLU HIS ALA LEU ALA ALA SEQRES 11 A 250 ALA LYS ALA GLY ARG ALA ALA ALA ALA GLN GLY LYS PHE SEQRES 12 A 250 ASP GLU PHE ARG LYS ALA LEU PHE GLU ALA SER ARG ASN SEQRES 13 A 250 VAL SER GLY HIS PRO ASN ASN THR LEU LYS ASP PHE GLU SEQRES 14 A 250 ARG PHE ALA ARG ASN ALA GLY VAL LYS ASP MSE GLU ARG SEQRES 15 A 250 PHE SER ARG GLU ALA GLN ASP SER THR TYR ASP GLU VAL SEQRES 16 A 250 LEU ALA LYS ALA ALA ASP TYR ALA HIS GLY LEU GLY VAL SEQRES 17 A 250 SER GLY THR PRO ALA PHE VAL VAL GLY THR GLN TYR ILE SEQRES 18 A 250 SER GLY ALA GLN PRO THR GLU GLU PHE ILE LYS VAL ILE SEQRES 19 A 250 GLU SER GLU LEU LYS LYS SER PRO THR PHE SER THR PRO SEQRES 20 A 250 SER SER HIS MODRES 4PWP MSE A 139 MET SELENOMETHIONINE MODRES 4PWP MSE A 141 MET SELENOMETHIONINE MODRES 4PWP MSE A 217 MET SELENOMETHIONINE HET MSE A 139 16 HET MSE A 141 8 HET MSE A 217 8 HET GOL A 301 6 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *231(H2 O) HELIX 1 1 PRO A 48 SER A 52 5 5 HELIX 2 2 LYS A 54 ASN A 59 1 6 HELIX 3 3 SER A 91 HIS A 99 5 9 HELIX 4 4 CYS A 126 THR A 136 1 11 HELIX 5 5 THR A 136 TYR A 144 1 9 HELIX 6 6 GLY A 161 GLN A 177 1 17 HELIX 7 7 LYS A 179 SER A 191 1 13 HELIX 8 8 THR A 201 GLY A 213 1 13 HELIX 9 9 ASP A 216 ALA A 224 1 9 HELIX 10 10 TYR A 229 GLY A 244 1 16 HELIX 11 11 PRO A 263 SER A 278 1 16 SHEET 1 A 5 ALA A 108 VAL A 109 0 SHEET 2 A 5 VAL A 150 ASP A 156 -1 O ILE A 152 N VAL A 109 SHEET 3 A 5 LEU A 116 SER A 122 1 N ILE A 118 O ARG A 151 SHEET 4 A 5 ALA A 250 VAL A 253 -1 O ALA A 250 N PHE A 121 SHEET 5 A 5 GLN A 256 SER A 259 -1 O GLN A 256 N VAL A 253 LINK C PRO A 138 N AMSE A 139 1555 1555 1.33 LINK C PRO A 138 N BMSE A 139 1555 1555 1.33 LINK C AMSE A 139 N LEU A 140 1555 1555 1.33 LINK C BMSE A 139 N LEU A 140 1555 1555 1.33 LINK C LEU A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N GLU A 142 1555 1555 1.33 LINK C ASP A 216 N MSE A 217 1555 1555 1.33 LINK C MSE A 217 N GLU A 218 1555 1555 1.34 CISPEP 1 THR A 248 PRO A 249 0 -4.93 SITE 1 AC1 7 ARG A 131 ALA A 261 PRO A 263 THR A 264 SITE 2 AC1 7 HOH A 414 HOH A 548 HOH A 619 CRYST1 48.819 68.435 69.139 90.00 90.00 90.00 P 21 21 21 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 0.020484 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014464 0.00000