10 20 30 40 50 60 70 80 2FXI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE, HYDROLASE 06-FEB-06 2FXI
TITLE ARSENATE REDUCTASE (ARSC FROM PI258) C10S/C15A DOUBLE TITLE 2 MUTANT WITH SULFATE IN ITS ACTIVE SITE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ARSC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ARSENATE REDUCTASE, ARSENICAL PUMP MODIFIER, LOW COMPND 5 MOLECULAR WEIGHT PROTEIN-TYROSINE-PHOSPHATASE; COMPND 6 EC: 1.20.4.-, 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: ARSC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PI258
KEYWDS ARSENATE REDUCTASE, REDOX ENZYME, OXIDOREDUCTASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.LORIS,L.BUTS,J.MESSENS
REVDAT 2 24-FEB-09 2FXI 1 VERSN REVDAT 1 08-AUG-06 2FXI 0
JRNL AUTH G.ROOS,L.BUTS,K.VAN BELLE,E.BROSENS,P.GEERLINGS, JRNL AUTH 2 R.LORIS,L.WYNS,J.MESSENS JRNL TITL INTERPLAY BETWEEN ION BINDING AND CATALYSIS IN THE JRNL TITL 2 THIOREDOXIN-COUPLED ARSENATE REDUCTASE FAMILY. JRNL REF J.MOL.BIOL. V. 360 826 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16797027 JRNL DOI 10.1016/J.JMB.2006.05.054
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 10780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 776 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 : 1017 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.60 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.31 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 2FXI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-06. REMARK 100 THE RCSB ID CODE IS RCSB036427.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-02 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 : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10780 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : 0.03700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.08000 REMARK 200 R SYM FOR SHELL (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.600 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: PDB ENTRY 1LJL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 8.0, 10 MM DTT, 100 REMARK 280 MM KCL, 10 MM K2SO4, 42.5% PEG-4000, 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 16.79550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.79350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.78950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.79350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.79550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.78950 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 CG SD CE REMARK 470 ASP A 2 OD1 OD2 REMARK 470 GLU A 26 CD OE1 OE2 REMARK 470 LYS A 53 CD CE NZ REMARK 470 ASN A 69 CG OD1 ND2 REMARK 470 LYS A 73 CD CE NZ REMARK 470 LYS A 109 CE NZ REMARK 470 LYS A 127 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 54.63 39.93 REMARK 500 ALA A 15 -73.18 -121.50 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 351 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 353 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A 368 DISTANCE = 9.70 ANGSTROMS
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 141 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 63 O REMARK 620 2 HOH A 250 O 69.0 REMARK 620 3 ASN A 13 OD1 71.0 134.6 REMARK 620 4 GLU A 21 OE2 107.5 58.5 117.0 REMARK 620 5 SER A 36 O 143.9 147.0 74.8 97.8 REMARK 620 6 SER A 36 OG 117.4 101.3 78.9 44.5 65.4 REMARK 620 7 HOH A 202 O 143.7 77.5 145.3 63.6 70.9 82.1 REMARK 620 8 ASP A 65 OD2 74.4 94.0 95.1 147.0 98.0 163.2 94.7 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 141 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 142
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LJL RELATED DB: PDB REMARK 900 WILD-TYPE ARSC
DBREF 2FXI A 1 131 UNP P0A006 ARSC_STAAU 1 131
SEQADV 2FXI SER A 10 UNP P0A006 CYS 10 ENGINEERED SEQADV 2FXI ALA A 15 UNP P0A006 CYS 15 ENGINEERED
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 CYS 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 141 1 HET SO4 A 142 5
HETNAM K POTASSIUM ION HETNAM SO4 SULFATE ION
FORMUL 2 K K 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *168(H2 O)
HELIX 1 1 ALA A 15 LEU A 28 1 14 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 CYS A 82 CYS A 89 1 8 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 K K A 141 O THR A 63 1555 1555 2.78 LINK K K A 141 O HOH A 250 1555 1555 3.00 LINK K K A 141 OD1 ASN A 13 1555 1555 2.94 LINK K K A 141 OE2 GLU A 21 1555 1555 3.52 LINK K K A 141 O SER A 36 1555 1555 2.86 LINK K K A 141 OG SER A 36 1555 1555 2.98 LINK K K A 141 O HOH A 202 1555 1555 2.90 LINK K K A 141 OD2 ASP A 65 1555 1555 2.95
SITE 1 AC1 7 ASN A 13 GLU A 21 SER A 36 THR A 63 SITE 2 AC1 7 ASP A 65 HOH A 202 HOH A 250 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 227
CRYST1 33.591 33.579 99.587 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 0.029770 0.000000 0.000000 0.00000
SCALE2 0.000000 0.029781 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010041 0.00000