HEADER OXIDOREDUCTASE 09-JAN-14 4OCE TITLE CRYSTAL STRUCTURE OF THE DISULFIDE OXIDOREDUCTASE DSBA FROM PROTEUS TITLE 2 MIRABILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEUS MIRABILIS HI4320; SOURCE 3 ORGANISM_TAXID: 529507; SOURCE 4 STRAIN: HI4320; SOURCE 5 GENE: DSBA, PMI2828; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS KEYWDS OXIDATIVE FOLDING PROTEIN, VIRULENCE FACTOR MATURATION PROTEIN, KEYWDS 2 DISULFIDE OXIDOREDUCTASE, THIOREDOXIN FOLD, DSBA, DITHIOL EXCHANGE, KEYWDS 3 DSBB, PERIPLASMIC, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.KURTH,J.L.MARTIN REVDAT 4 20-SEP-23 4OCE 1 REMARK SEQADV REVDAT 3 22-NOV-17 4OCE 1 REMARK REVDAT 2 30-JUL-14 4OCE 1 JRNL REVDAT 1 28-MAY-14 4OCE 0 JRNL AUTH F.KURTH,W.DUPREZ,L.PREMKUMAR,M.A.SCHEMBRI,D.P.FAIRLIE, JRNL AUTH 2 J.L.MARTIN JRNL TITL CRYSTAL STRUCTURE OF THE DITHIOL OXIDASE DSBA ENZYME FROM JRNL TITL 2 PROTEUS MIRABILIS BOUND NON-COVALENTLY TO AN ACTIVE SITE JRNL TITL 3 PEPTIDE LIGAND. JRNL REF J.BIOL.CHEM. V. 289 19810 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24831013 JRNL DOI 10.1074/JBC.M114.552380 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22686 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1159 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 37.5381 - 3.5352 1.00 2965 158 0.1590 0.1616 REMARK 3 2 3.5352 - 2.8063 1.00 2763 133 0.1478 0.1522 REMARK 3 3 2.8063 - 2.4516 1.00 2684 151 0.1420 0.1629 REMARK 3 4 2.4516 - 2.2275 1.00 2601 154 0.1333 0.1774 REMARK 3 5 2.2275 - 2.0679 1.00 2644 161 0.1319 0.1640 REMARK 3 6 2.0679 - 1.9460 1.00 2651 139 0.1432 0.1891 REMARK 3 7 1.9460 - 1.8485 1.00 2604 134 0.1485 0.1922 REMARK 3 8 1.8485 - 1.7680 1.00 2615 129 0.1729 0.2190 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.20 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 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 : 0.009 1531 REMARK 3 ANGLE : 1.152 2078 REMARK 3 CHIRALITY : 0.065 229 REMARK 3 PLANARITY : 0.006 277 REMARK 3 DIHEDRAL : 14.174 566 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 4OCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 0.95369 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.768 REMARK 200 RESOLUTION RANGE LOW (A) : 42.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 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: 1DSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, SODIUM MALONATE, PH 5.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 149.22500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.91500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 223.83750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.91500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.91500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.61250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.91500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.91500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 223.83750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.91500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.91500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.61250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 149.22500 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 420 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 LYS A 188 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 14 CD CE NZ REMARK 480 LYS A 41 CE NZ REMARK 480 LYS A 48 CE NZ REMARK 480 GLU A 52 CG CD OE1 OE2 REMARK 480 LYS A 168 CD CE NZ 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 -75.20 -102.64 REMARK 500 LYS A 157 -35.60 -132.16 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 MLI A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OCF RELATED DB: PDB REMARK 900 PROTEUS MIRABLIS DSBA (CYS30SER) REMARK 900 RELATED ID: 4OD7 RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF PROTEUS MIRABLIS DSBA (C30S) WITH A NON- REMARK 900 COVALENTLY BOUND PEPTIDE PWATCDS DBREF 4OCE A -1 188 UNP B4EZ68 B4EZ68_PROMH 18 207 SEQADV 4OCE ASN A 0 UNP B4EZ68 ALA 19 ENGINEERED MUTATION SEQRES 1 A 190 SER ASN ALA ASP ILE SER GLU GLY LYS GLN TYR THR ASN SEQRES 2 A 190 LEU SER LYS PRO VAL ALA GLY ALA PRO GLN VAL VAL GLU SEQRES 3 A 190 PHE PHE SER PHE TYR CYS PRO HIS CYS TYR GLN PHE SER SEQRES 4 A 190 GLU VAL TYR LYS VAL ASN SER THR VAL GLU LYS ASN VAL SEQRES 5 A 190 PRO GLU ASN THR LYS MET ALA ARG TYR HIS VAL ASP PHE SEQRES 6 A 190 LEU GLY PRO LEU GLY LYS GLU MET THR ARG ALA TRP ALA SEQRES 7 A 190 VAL ALA ILE ALA LEU GLY VAL GLU ASP GLN VAL SER PRO SEQRES 8 A 190 ALA LEU PHE LYS GLY ILE GLN GLU THR GLN SER ILE ARG SEQRES 9 A 190 SER VAL ASP ASP ILE ARG THR THR PHE ILE ASN ALA GLY SEQRES 10 A 190 VAL LYS ALA GLU ASP TYR ASP ALA ALA ILE ASN SER PHE SEQRES 11 A 190 VAL VAL ASN SER LEU VAL SER GLN GLN GLN ASN ALA VAL SEQRES 12 A 190 THR ASP PHE GLN ILE ASN GLY VAL PRO ALA MET VAL ILE SEQRES 13 A 190 ASP GLY LYS TYR LYS MET LYS ASN ASP GLY ILE SER ALA SEQRES 14 A 190 LYS SER PRO GLU GLU TYR ALA LYS ALA TYR SER ASP VAL SEQRES 15 A 190 VAL ASN GLN LEU LEU MET LYS LYS HET MLI A 201 7 HETNAM MLI MALONATE ION FORMUL 2 MLI C3 H2 O4 2- FORMUL 3 HOH *268(H2 O) HELIX 1 1 CYS A 30 VAL A 39 1 10 HELIX 2 2 LYS A 41 VAL A 50 1 10 HELIX 3 3 LEU A 67 GLY A 82 1 16 HELIX 4 4 VAL A 83 GLU A 97 1 15 HELIX 5 5 SER A 103 ALA A 114 1 12 HELIX 6 6 LYS A 117 ILE A 125 1 9 HELIX 7 7 SER A 127 PHE A 144 1 18 HELIX 8 8 SER A 169 MET A 186 1 18 SHEET 1 A 5 TYR A 9 ASN A 11 0 SHEET 2 A 5 TYR A 158 MET A 160 -1 O LYS A 159 N THR A 10 SHEET 3 A 5 ALA A 151 ILE A 154 -1 N ILE A 154 O TYR A 158 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 2.03 CISPEP 1 VAL A 149 PRO A 150 0 -5.15 SITE 1 AC1 8 TYR A 40 VAL A 42 SER A 127 PHE A 128 SITE 2 AC1 8 VAL A 129 PRO A 170 TYR A 173 HOH A 305 CRYST1 37.830 37.830 298.450 90.00 90.00 90.00 P 43 21 2 8 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 0.026434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003351 0.00000