HEADER UNKNOWN FUNCTION 01-AUG-11 3T8T TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS CYMR OXIDIZED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAPHYLOCOCCUS AUREUS CYMR (OXIDIZED FORM); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50; SOURCE 5 ATCC: 700699; SOURCE 6 GENE: SAV1626; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL REGULATOR PROTEIN, DIMER, SULFENIC ACID, UNKNOWN KEYWDS 2 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.HE,Q.JI REVDAT 2 18-JUL-12 3T8T 1 JRNL REVDAT 1 16-MAY-12 3T8T 0 JRNL AUTH Q.JI,L.ZHANG,F.SUN,X.DENG,H.LIANG,T.BAE,C.HE JRNL TITL STAPHYLOCOCCUS AUREUS CYMR IS A NEW THIOL-BASED JRNL TITL 2 OXIDATION-SENSING REGULATOR OF STRESS RESISTANCE AND JRNL TITL 3 OXIDATIVE RESPONSE. JRNL REF J.BIOL.CHEM. V. 287 21102 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22553203 JRNL DOI 10.1074/JBC.M112.359737 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 13355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2324 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 19.1395 - 3.7666 1.00 2366 261 0.1952 0.2211 REMARK 3 2 3.7666 - 2.9933 0.99 2334 261 0.2031 0.2212 REMARK 3 3 2.9933 - 2.6160 0.97 2297 258 0.2114 0.2342 REMARK 3 4 2.6160 - 2.3773 0.95 2244 245 0.2101 0.2427 REMARK 3 5 2.3773 - 2.2072 0.94 2208 248 0.2082 0.2633 REMARK 3 6 2.2072 - 2.0772 0.90 2093 235 0.2060 0.2810 REMARK 3 7 2.0772 - 1.9733 0.88 2092 228 0.2315 0.3316 REMARK 3 8 1.9733 - 1.8875 0.83 1961 210 0.2659 0.3105 REMARK 3 9 1.8875 - 1.8149 0.77 1861 194 0.2892 0.3242 REMARK 3 10 1.8149 - 1.7520 0.71 1645 184 0.2908 0.3489 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 : 0.40 REMARK 3 B_SOL : 61.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.060 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) : 2.24650 REMARK 3 B22 (A**2) : -0.07490 REMARK 3 B33 (A**2) : -2.17160 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : 8.98230 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 : 0.007 973 REMARK 3 ANGLE : 1.046 1307 REMARK 3 CHIRALITY : 0.079 151 REMARK 3 PLANARITY : 0.006 167 REMARK 3 DIHEDRAL : 14.337 382 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 3T8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-11. REMARK 100 THE RCSB ID CODE IS RCSB067181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.752 REMARK 200 RESOLUTION RANGE LOW (A) : 19.138 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M LITHIUM SULFATE MONOHYDRATE, 0.1M REMARK 280 SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 12% PEG6000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 38.66400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.28800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.66400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.28800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 77.32800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 PRO A 86 REMARK 465 ILE A 87 REMARK 465 THR A 88 REMARK 465 PHE A 89 REMARK 465 VAL A 90 REMARK 465 SER A 130 REMARK 465 GLU A 131 REMARK 465 ASP A 132 REMARK 465 LEU A 133 REMARK 465 ASP A 134 REMARK 465 GLY A 135 REMARK 465 TYR A 136 REMARK 465 MET A 137 REMARK 465 PHE A 138 REMARK 465 TYR A 139 REMARK 465 ILE A 140 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 LYS A 2 N - CA - C ANGL. DEV. = -18.1 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 LYS A 2 169.11 168.83 REMARK 500 GLU A 21 133.31 -37.90 REMARK 500 GLN A 23 -22.24 -142.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LYS A 2 46.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T8R RELATED DB: PDB DBREF 3T8T A 1 140 UNP Q99TM3 Q99TM3_STAAM 1 140 SEQADV 3T8T SER A -2 UNP Q99TM3 EXPRESSION TAG SEQADV 3T8T ASN A -1 UNP Q99TM3 EXPRESSION TAG SEQADV 3T8T ALA A 0 UNP Q99TM3 EXPRESSION TAG SEQRES 1 A 143 SER ASN ALA MET LYS ILE SER THR LYS GLY ARG TYR GLY SEQRES 2 A 143 LEU THR LEU MET ILE SER LEU ALA LYS LYS GLU GLY GLN SEQRES 3 A 143 GLY CSO ILE SER LEU LYS SER ILE ALA GLU GLU ASN ASN SEQRES 4 A 143 LEU SER ASP LEU TYR LEU GLU GLN LEU VAL GLY PRO LEU SEQRES 5 A 143 ARG ASN ALA GLY LEU ILE ARG SER VAL ARG GLY ALA LYS SEQRES 6 A 143 GLY GLY TYR GLN LEU ARG VAL PRO ALA GLU GLU ILE SER SEQRES 7 A 143 ALA GLY ASP ILE ILE ARG LEU LEU GLU GLY PRO ILE THR SEQRES 8 A 143 PHE VAL GLU SER ILE GLU SER GLU PRO PRO ALA GLN LYS SEQRES 9 A 143 GLN LEU TRP ILE ARG MET ARG ASP ALA VAL ARG ASP VAL SEQRES 10 A 143 LEU ASP ASN THR THR LEU LYS TYR LEU ALA GLU TYR VAL SEQRES 11 A 143 ASP THR SER GLU ASP LEU ASP GLY TYR MET PHE TYR ILE MODRES 3T8T CSO A 25 CYS S-HYDROXYCYSTEINE HET CSO A 25 7 HETNAM CSO S-HYDROXYCYSTEINE FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 HOH *59(H2 O) HELIX 1 1 SER A 4 LYS A 19 1 16 HELIX 2 2 LEU A 28 ASN A 35 1 8 HELIX 3 3 SER A 38 ALA A 52 1 15 HELIX 4 4 PRO A 70 ILE A 74 5 5 HELIX 5 5 SER A 75 GLY A 85 1 11 HELIX 6 6 PRO A 97 ASN A 117 1 21 HELIX 7 7 THR A 119 TYR A 126 1 8 SHEET 1 A 3 ILE A 26 SER A 27 0 SHEET 2 A 3 GLY A 64 LEU A 67 -1 O TYR A 65 N ILE A 26 SHEET 3 A 3 ILE A 55 SER A 57 -1 N ARG A 56 O GLN A 66 LINK C GLY A 24 N CSO A 25 1555 1555 1.33 LINK C CSO A 25 N ILE A 26 1555 1555 1.33 CISPEP 1 MET A 1 LYS A 2 0 21.50 CRYST1 77.328 52.576 33.449 90.00 98.12 90.00 C 1 2 1 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 0.012932 0.000000 0.001844 0.00000 SCALE2 0.000000 0.019020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030199 0.00000