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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
