HEADER OXIDOREDUCTASE 18-DEC-03 1RXE TITLE ARSC COMPLEXED WITH MNB COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARSENATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ARSC, ARSENICAL PUMP MODIFIER; COMPND 5 EC: 1.20.4.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: ARSC, SAP018; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARSC, MIXED DISULPHIDE, 5-THIO-2-NITROBENZOIC ACID, 5-MERCAPTO-2- KEYWDS 2 NITROBENZOIC ACID, TNB, MNB, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MESSENS,I.VAN MOLLE,P.VANHAESEBROUCK,M.LIMBOURG,K.VAN BELLE, AUTHOR 2 K.WAHNI,J.C.MARTINS,R.LORIS,L.WYNS REVDAT 3 27-OCT-21 1RXE 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1RXE 1 VERSN REVDAT 1 01-JUN-04 1RXE 0 JRNL AUTH J.MESSENS,I.VAN MOLLE,P.VANHAESEBROUCK,K.VAN BELLE,K.WAHNI, JRNL AUTH 2 J.C.MARTINS,L.WYNS,R.LORIS JRNL TITL THE STRUCTURE OF A TRIPLE MUTANT OF PI258 ARSENATE REDUCTASE JRNL TITL 2 FROM STAPHYLOCOCCUS AUREUS AND ITS 5-THIO-2-NITROBENZOIC JRNL TITL 3 ACID ADDUCT. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 1180 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 15159594 JRNL DOI 10.1107/S0907444904007334 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11893 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 960 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1022 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 125 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) : 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.440 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11893 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.1 REMARK 200 DATA REDUNDANCY : 3.130 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.26 REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM CHLORIDE, SODIUM REMARK 280 PERCHLORATE, PEG4000, TRIS, PH 8.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.57300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.16250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.18850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.16250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.57300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.18850 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 N CB CG SD CE REMARK 470 ASP A 70 CG OD1 OD2 REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 97 CG 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 ASN A 13 61.31 -115.27 REMARK 500 SER A 14 -51.13 -120.87 REMARK 500 ALA A 15 -75.40 -118.87 REMARK 500 THR A 41 -74.31 -84.49 REMARK 500 HIS A 42 -5.27 78.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 152 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 13 OD1 REMARK 620 2 GLU A 21 OE2 121.2 REMARK 620 3 SER A 36 O 71.8 104.3 REMARK 620 4 SER A 36 OG 79.8 50.5 63.9 REMARK 620 5 THR A 63 O 71.9 110.2 139.1 126.0 REMARK 620 6 ASP A 65 OD2 89.9 148.4 90.0 153.8 71.7 REMARK 620 7 HOH A 205 O 142.4 75.4 71.3 90.5 138.2 83.1 REMARK 620 8 HOH A 207 O 142.0 68.2 145.2 118.7 70.6 83.9 74.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LCP A 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MNB A 151 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LJL RELATED DB: PDB REMARK 900 WILD-TYPE ARSC IN ITS REDUCED STATE REMARK 900 RELATED ID: 1RXI RELATED DB: PDB REMARK 900 ARSC TRIPLE MUTANT C10S/C15A/C82S DBREF 1RXE A 1 131 UNP P0A006 ARSC_STAAU 1 131 SEQADV 1RXE SER A 10 UNP P0A006 CYS 10 ENGINEERED MUTATION SEQADV 1RXE ALA A 15 UNP P0A006 CYS 15 ENGINEERED MUTATION SEQADV 1RXE SER A 82 UNP P0A006 CYS 82 ENGINEERED MUTATION SEQRES 1 A 131 MET ASP LYS LYS THR ILE TYR PHE ILE SER THR GLY ASN SEQRES 2 A 131 SER ALA ARG SER GLN MET ALA GLU GLY TRP GLY LYS GLU SEQRES 3 A 131 ILE LEU GLY GLU GLY TRP ASN VAL TYR SER ALA GLY ILE SEQRES 4 A 131 GLU THR HIS GLY VAL ASN PRO LYS ALA ILE GLU ALA MET SEQRES 5 A 131 LYS GLU VAL ASP ILE ASP ILE SER ASN HIS THR SER ASP SEQRES 6 A 131 LEU ILE ASP ASN ASP ILE LEU LYS GLN SER ASP LEU VAL SEQRES 7 A 131 VAL THR LEU SER SER ASP ALA ASP ASN ASN CYS PRO ILE SEQRES 8 A 131 LEU PRO PRO ASN VAL LYS LYS GLU HIS TRP GLY PHE ASP SEQRES 9 A 131 ASP PRO ALA GLY LYS GLU TRP SER GLU PHE GLN ARG VAL SEQRES 10 A 131 ARG ASP GLU ILE LYS LEU ALA ILE GLU LYS PHE LYS LEU SEQRES 11 A 131 ARG HET K A 152 1 HET LCP A 153 5 HET MNB A 151 13 HETNAM K POTASSIUM ION HETNAM LCP PERCHLORATE ION HETNAM MNB 5-MERCAPTO-2-NITRO-BENZOIC ACID FORMUL 2 K K 1+ FORMUL 3 LCP CL O4 1- FORMUL 4 MNB C7 H5 N O4 S FORMUL 5 HOH *125(H2 O) HELIX 1 1 ALA A 15 GLY A 29 1 15 HELIX 2 2 ASN A 45 VAL A 55 1 11 HELIX 3 3 ASP A 68 GLN A 74 1 7 HELIX 4 4 SER A 82 ASN A 88 1 7 HELIX 5 5 GLU A 110 LEU A 130 1 21 SHEET 1 A 4 TRP A 32 GLY A 38 0 SHEET 2 A 4 LYS A 4 SER A 10 1 N LYS A 4 O ASN A 33 SHEET 3 A 4 LEU A 77 THR A 80 1 O VAL A 79 N ILE A 9 SHEET 4 A 4 LYS A 97 HIS A 100 1 O GLU A 99 N VAL A 78 LINK SG CYS A 89 S5 MNB A 151 1555 1555 2.04 LINK OD1 ASN A 13 K K A 152 1555 1555 2.85 LINK OE2 GLU A 21 K K A 152 1555 1555 2.90 LINK O SER A 36 K K A 152 1555 1555 2.96 LINK OG SER A 36 K K A 152 1555 1555 2.94 LINK O THR A 63 K K A 152 1555 1555 2.80 LINK OD2 ASP A 65 K K A 152 1555 1555 2.88 LINK K K A 152 O HOH A 205 1555 1555 2.84 LINK K K A 152 O HOH A 207 1555 1555 3.36 SITE 1 AC1 6 ASN A 13 GLU A 21 SER A 36 THR A 63 SITE 2 AC1 6 ASP A 65 HOH A 205 SITE 1 AC2 8 SER A 10 THR A 11 GLY A 12 SER A 14 SITE 2 AC2 8 ALA A 15 ARG A 16 SER A 17 HOH A 201 SITE 1 AC3 8 ILE A 39 ILE A 67 ALA A 85 ASN A 88 SITE 2 AC3 8 CYS A 89 PRO A 90 HOH A 215 HOH A 325 CRYST1 33.146 34.377 102.325 90.00 90.00 90.00 P 21 21 21 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 0.030170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009773 0.00000