HEADER OXIDOREDUCTASE 05-JAN-10 3L9S TITLE CRYSTAL STRUCTURE OF SALMONELLA ENTERICA SEROVAR TYPHIMURIUM DSBA COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-207; COMPND 5 EC: 5.3.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM; SOURCE 4 ORGANISM_TAXID: 216597; SOURCE 5 STRAIN: SL1344; SOURCE 6 GENE: DSBA, STM3997; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)/PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PETLIC KEYWDS THIOREDOXIN-FOLD, DSBA, THIOL-DISULFIDE OXIDOREDUCTASE, DISULFIDE KEYWDS 2 BOND, REDOX-ACTIVE CENTER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.HERAS,R.JARROTT,S.R.SHOULDICE,G.GUNCAR REVDAT 4 01-NOV-23 3L9S 1 SEQADV REVDAT 3 01-NOV-17 3L9S 1 REMARK REVDAT 2 16-FEB-11 3L9S 1 JRNL DBREF SEQADV REMARK REVDAT 1 09-MAR-10 3L9S 0 JRNL AUTH B.HERAS,M.TOTSIKA,R.JARROTT,S.R.SHOULDICE,G.GUNCAR, JRNL AUTH 2 M.E.S.ACHARD,T.J.WELLS,M.P.ARGENTE,A.G.MCEWAN,M.A.SCHEMBRI JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THREE DSBA JRNL TITL 2 PARALOGUES FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM JRNL REF J.BIOL.CHEM. V. 285 18423 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20233716 JRNL DOI 10.1074/JBC.M110.101360 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 25095 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1279 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 21.0590 - 3.2830 0.80 2258 138 0.1770 0.1880 REMARK 3 2 3.2830 - 2.6070 0.96 2697 139 0.1550 0.1990 REMARK 3 3 2.6070 - 2.2780 0.98 2727 146 0.1410 0.1840 REMARK 3 4 2.2780 - 2.0700 0.98 2723 137 0.1250 0.2100 REMARK 3 5 2.0700 - 1.9220 0.98 2737 151 0.1190 0.1710 REMARK 3 6 1.9220 - 1.8090 0.98 2707 147 0.1140 0.1760 REMARK 3 7 1.8090 - 1.7180 0.98 2671 145 0.1060 0.1830 REMARK 3 8 1.7180 - 1.6430 0.98 2708 135 0.1080 0.1470 REMARK 3 9 1.6430 - 1.5800 0.92 2588 141 0.1080 0.1740 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 : 0.41 REMARK 3 B_SOL : 60.27 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.54600 REMARK 3 B22 (A**2) : 8.33900 REMARK 3 B33 (A**2) : 2.20700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.44200 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 1559 REMARK 3 ANGLE : 0.903 2126 REMARK 3 CHIRALITY : 0.059 235 REMARK 3 PLANARITY : 0.004 280 REMARK 3 DIHEDRAL : 18.199 567 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 3L9S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.956667 REMARK 200 MONOCHROMATOR : DOUBLE SI WITH SAGITTALY BENT REMARK 200 SECOND CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25131 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18800 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: PHASER 1.3.3 REMARK 200 STARTING MODEL: PDB ENTRY 1FVK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M AMMONIUM SULFATE, 1% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3350, 100MM 2,2-BIS(HYDROXYMETHYL)-2,2',2"- REMARK 280 NITRILOTRIETHANOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 30.91850 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 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 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 ALA A 1 REMARK 465 GLN A 2 REMARK 465 LYS A 188 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 -86.05 -102.72 REMARK 500 LYS A 97 -67.26 -101.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H93 RELATED DB: PDB REMARK 900 RELATED ID: 3A3T RELATED DB: PDB REMARK 900 RELATED ID: 3F4R RELATED DB: PDB REMARK 900 RELATED ID: 3BCI RELATED DB: PDB REMARK 900 RELATED ID: 1FVK RELATED DB: PDB REMARK 900 RELATED ID: 1DSB RELATED DB: PDB REMARK 900 RELATED ID: 3L9U RELATED DB: PDB REMARK 900 RELATED ID: 3L9V RELATED DB: PDB DBREF 3L9S A 0 188 UNP E1WE53 E1WE53_SALTY 19 207 SEQADV 3L9S SER A -2 UNP E1WE53 EXPRESSION TAG SEQADV 3L9S ASN A -1 UNP E1WE53 EXPRESSION TAG SEQRES 1 A 191 SER ASN ALA ALA GLN ILE SER ASP GLY LYS GLN TYR ILE SEQRES 2 A 191 THR LEU ASP LYS PRO VAL ALA GLY GLU PRO GLN VAL LEU SEQRES 3 A 191 GLU PHE PHE SER PHE TYR CYS PRO HIS CYS TYR GLN PHE SEQRES 4 A 191 GLU GLU VAL LEU HIS VAL SER ASP ASN VAL LYS LYS LYS SEQRES 5 A 191 LEU PRO GLU GLY THR LYS MET THR LYS TYR HIS VAL GLU SEQRES 6 A 191 PHE LEU GLY PRO LEU GLY LYS GLU LEU THR GLN ALA TRP SEQRES 7 A 191 ALA VAL ALA MET ALA LEU GLY VAL GLU ASP LYS VAL THR SEQRES 8 A 191 VAL PRO LEU PHE GLU ALA VAL GLN LYS THR GLN THR VAL SEQRES 9 A 191 GLN SER ALA ALA ASP ILE ARG LYS VAL PHE VAL ASP ALA SEQRES 10 A 191 GLY VAL LYS GLY GLU ASP TYR ASP ALA ALA TRP ASN SER SEQRES 11 A 191 PHE VAL VAL LYS SER LEU VAL ALA GLN GLN GLU LYS ALA SEQRES 12 A 191 ALA ALA ASP LEU GLN LEU GLN GLY VAL PRO ALA MET PHE SEQRES 13 A 191 VAL ASN GLY LYS TYR GLN ILE ASN PRO GLN GLY MET ASP SEQRES 14 A 191 THR SER SER MET ASP VAL PHE VAL GLN GLN TYR ALA ASP SEQRES 15 A 191 THR VAL LYS TYR LEU VAL ASP LYS LYS FORMUL 2 HOH *259(H2 O) HELIX 1 1 CYS A 30 VAL A 39 1 10 HELIX 2 2 HIS A 41 LEU A 50 1 10 HELIX 3 3 LEU A 67 GLY A 82 1 16 HELIX 4 4 VAL A 83 LYS A 97 1 15 HELIX 5 5 SER A 103 ALA A 114 1 12 HELIX 6 6 LYS A 117 ASN A 126 1 10 HELIX 7 7 SER A 127 LEU A 144 1 18 HELIX 8 8 PRO A 162 MET A 165 5 4 HELIX 9 9 SER A 169 LYS A 187 1 19 SHEET 1 A 5 TYR A 9 THR A 11 0 SHEET 2 A 5 TYR A 158 ILE A 160 -1 O GLN A 159 N ILE A 10 SHEET 3 A 5 ALA A 151 VAL A 154 -1 N MET A 152 O ILE A 160 SHEET 4 A 5 VAL A 22 PHE A 26 -1 N PHE A 25 O ALA A 151 SHEET 5 A 5 MET A 56 HIS A 60 1 O TYR A 59 N GLU A 24 SSBOND 1 CYS A 30 CYS A 33 1555 1555 2.04 CISPEP 1 VAL A 149 PRO A 150 0 -2.94 CRYST1 37.377 61.837 42.951 90.00 101.32 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 0.026754 0.000000 0.005356 0.00000 SCALE2 0.000000 0.016172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023744 0.00000