HEADER OXIDOREDUCTASE 05-JAN-10 3L9U TITLE CRYSTAL STRUCTURE OF SALMONELLA ENTERICA SEROVAR TYPHIMURIUM DSBL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISULFIDE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-223; COMPND 5 SYNONYM: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBL; COMPND 6 EC: 5.3.4.1; COMPND 7 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: DSBL, STM3193; 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, DSBL, THIOL-DISULFIDE OXIDOREDUCTASE, ISOMERASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.HERAS,R.JARROTT,S.R.SHOULDICE,G.GUNCAR REVDAT 4 01-NOV-23 3L9U 1 SEQADV REVDAT 3 01-NOV-17 3L9U 1 REMARK REVDAT 2 16-FEB-11 3L9U 1 JRNL DBREF REMARK SEQADV REVDAT 1 09-MAR-10 3L9U 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. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34443 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1745 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 28.4090 - 3.3770 0.99 3463 176 0.1480 0.1560 REMARK 3 2 3.3770 - 2.6810 1.00 3310 196 0.1590 0.2090 REMARK 3 3 2.6810 - 2.3420 1.00 3272 180 0.1600 0.1920 REMARK 3 4 2.3420 - 2.1280 1.00 3284 153 0.1330 0.1640 REMARK 3 5 2.1280 - 1.9760 1.00 3263 185 0.1260 0.1760 REMARK 3 6 1.9760 - 1.8590 1.00 3225 176 0.1250 0.1620 REMARK 3 7 1.8590 - 1.7660 1.00 3232 170 0.1260 0.1750 REMARK 3 8 1.7660 - 1.6890 1.00 3233 174 0.1290 0.1940 REMARK 3 9 1.6890 - 1.6240 1.00 3211 180 0.1310 0.1650 REMARK 3 10 1.6240 - 1.5680 0.99 3205 155 0.1390 0.2170 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 : 54.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 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) : 19.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.90300 REMARK 3 B22 (A**2) : -1.86700 REMARK 3 B33 (A**2) : -5.03600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.006 1655 REMARK 3 ANGLE : 0.944 2245 REMARK 3 CHIRALITY : 0.065 243 REMARK 3 PLANARITY : 0.004 286 REMARK 3 DIHEDRAL : 17.420 603 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 3L9U 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_1000057014. 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 : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 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 : NULL 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 : 34491 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.568 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3C7M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6-3.4 M SODIUM MALONATE PH 7.0 -7.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 42.79100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.29650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.79100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.29650 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 288 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 298 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 300 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 427 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 ASN A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 32 CA - CB - SG ANGL. DEV. = 7.5 DEGREES 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 164 27.97 -143.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C7M 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: 3L9S RELATED DB: PDB REMARK 900 RELATED ID: 3L9V RELATED DB: PDB DBREF 3L9U A 1 199 UNP E1WHY0 E1WHY0_SALTY 25 223 SEQADV 3L9U SER A -1 UNP E1WHY0 EXPRESSION TAG SEQADV 3L9U ASN A 0 UNP E1WHY0 EXPRESSION TAG SEQRES 1 A 201 SER ASN ALA SER ALA PHE THR GLU GLY THR ASP TYR MET SEQRES 2 A 201 VAL LEU GLU LYS PRO ILE PRO ASN ALA ASP LYS THR LEU SEQRES 3 A 201 ILE LYS VAL PHE SER TYR ALA CYS PRO PHE CYS TYR LYS SEQRES 4 A 201 TYR ASP LYS ALA VAL THR GLY PRO VAL SER ASP LYS VAL SEQRES 5 A 201 ALA ASP LEU VAL THR PHE THR PRO PHE HIS LEU GLU THR SEQRES 6 A 201 LYS GLY GLU TYR GLY LYS GLN ALA SER GLU VAL PHE ALA SEQRES 7 A 201 VAL LEU ILE ALA LYS ASP LYS ALA ALA GLY ILE SER LEU SEQRES 8 A 201 PHE ASP ALA LYS SER GLN PHE LYS LYS ALA LYS PHE ALA SEQRES 9 A 201 TRP TYR ALA ALA TYR HIS ASP LYS LYS GLU ARG TRP SER SEQRES 10 A 201 ASP GLY LYS ASP PRO ALA ALA PHE ILE LYS THR GLY LEU SEQRES 11 A 201 ASP ALA ALA GLY MET SER GLN ALA ASP PHE GLU ALA ALA SEQRES 12 A 201 LEU LYS ASP PRO ALA VAL GLN GLU THR LEU GLU LYS TRP SEQRES 13 A 201 LYS ALA ALA TYR ASP VAL ALA LYS ILE GLN GLY VAL PRO SEQRES 14 A 201 ALA TYR VAL VAL ASN GLY LYS TYR LEU ILE TYR THR LYS SEQRES 15 A 201 ASN ILE LYS SER ILE ASP SER MET ALA GLU LEU VAL ARG SEQRES 16 A 201 GLU LEU ALA THR LYS LYS FORMUL 2 HOH *299(H2 O) HELIX 1 1 CYS A 32 VAL A 42 1 11 HELIX 2 2 VAL A 42 ALA A 51 1 10 HELIX 3 3 TYR A 67 ALA A 85 1 19 HELIX 4 4 SER A 94 ASP A 109 1 16 HELIX 5 5 ARG A 113 LYS A 118 5 6 HELIX 6 6 ASP A 119 GLY A 132 1 14 HELIX 7 7 SER A 134 LEU A 142 1 9 HELIX 8 8 ASP A 144 TRP A 154 1 11 HELIX 9 9 ALA A 156 GLY A 165 1 10 HELIX 10 10 THR A 179 ILE A 182 5 4 HELIX 11 11 SER A 184 THR A 197 1 14 SHEET 1 A 5 TYR A 10 VAL A 12 0 SHEET 2 A 5 TYR A 175 ILE A 177 -1 O LEU A 176 N MET A 11 SHEET 3 A 5 ALA A 168 VAL A 171 -1 N TYR A 169 O ILE A 177 SHEET 4 A 5 THR A 23 PHE A 28 -1 N VAL A 27 O ALA A 168 SHEET 5 A 5 THR A 55 HIS A 60 1 O THR A 57 N LEU A 24 SSBOND 1 CYS A 32 CYS A 35 1555 1555 2.03 CISPEP 1 VAL A 166 PRO A 167 0 2.24 CRYST1 85.582 46.593 60.222 90.00 90.00 90.00 P 21 21 2 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 0.011685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016605 0.00000