HEADER STRUCTURAL GENOMICS 21-MAR-14 4PWO 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, DISULFIDED 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 2 08-NOV-23 4PWO 1 REMARK REVDAT 1 25-MAR-15 4PWO 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. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34302 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1801 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 19.9348 - 3.5671 0.99 2783 149 0.1537 0.1585 REMARK 3 2 3.5671 - 2.8339 1.00 2695 137 0.1728 0.1883 REMARK 3 3 2.8339 - 2.4764 1.00 2666 138 0.1807 0.2187 REMARK 3 4 2.4764 - 2.2504 1.00 2646 153 0.1708 0.1963 REMARK 3 5 2.2504 - 2.0892 1.00 2627 139 0.1595 0.1877 REMARK 3 6 2.0892 - 1.9662 1.00 2637 135 0.1693 0.1992 REMARK 3 7 1.9662 - 1.8678 1.00 2602 154 0.1711 0.2275 REMARK 3 8 1.8678 - 1.7865 1.00 2624 130 0.1654 0.2170 REMARK 3 9 1.7865 - 1.7178 1.00 2638 126 0.1648 0.1949 REMARK 3 10 1.7178 - 1.6586 1.00 2593 141 0.1679 0.2117 REMARK 3 11 1.6586 - 1.6067 1.00 2604 138 0.1731 0.2558 REMARK 3 12 1.6067 - 1.5608 1.00 2593 136 0.1710 0.2143 REMARK 3 13 1.5608 - 1.5197 0.99 2590 125 0.1773 0.2276 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.610 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 2047 REMARK 3 ANGLE : 1.068 2799 REMARK 3 CHIRALITY : 0.072 304 REMARK 3 PLANARITY : 0.005 378 REMARK 3 DIHEDRAL : 13.515 783 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 4PWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : 36061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.8 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) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COOT REMARK 200 STARTING MODEL: 4PWP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE, 0.1M TRIS-HCL PH REMARK 280 8.5, 30% PEG4K, VAPOR DIFFUSION, 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 24.31900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.59650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.15900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.59650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.31900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.15900 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: 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 46.38 -101.89 REMARK 500 TYR A 144 -54.22 -129.20 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: 4PWP 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. DBREF 4PWO A 38 287 PDB 4PWO 4PWO 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 ALA 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 THR LEU MET 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 MET 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 HET GOL A 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *195(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 LEU A 243 1 15 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 CISPEP 1 THR A 248 PRO A 249 0 -6.57 SITE 1 AC1 8 ARG A 131 GLN A 135 ALA A 261 PRO A 263 SITE 2 AC1 8 THR A 264 GLU A 265 HOH A 414 HOH A 587 CRYST1 48.638 68.318 69.193 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 0.020560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014452 0.00000