10 20 30 40 50 60 70 80 2O89 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 12-DEC-06 2O89
TITLE S. AUREUS THIOREDOXIN P31T/C32S MUTANT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRX; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: TRXA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-14B
KEYWDS THIOREDOXIN, REDOX ENZYME, OXIDOREDUCTASE, ELECTRON KEYWDS 2 TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR G.ROOS,R.LORIS,J.MESSENS
REVDAT 2 24-FEB-09 2O89 1 VERSN REVDAT 1 24-JUL-07 2O89 0
JRNL AUTH G.ROOS,A.GARCIA-PINO,K.VAN BELLE,E.BROSENS,K.WAHNI, JRNL AUTH 2 G.VANDENBUSSCHE,L.WYNS,R.LORIS,J.MESSENS JRNL TITL THE CONSERVED ACTIVE SITE PROLINE DETERMINES THE JRNL TITL 2 REDUCING POWER OF STAPHYLOCOCCUS AUREUS THIOREDOXIN JRNL REF J.MOL.BIOL. V. 368 800 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17368484 JRNL DOI 10.1016/J.JMB.2007.02.045
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 3913 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) : 0.202 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 429 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 : 758 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.34 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 2O89 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-06. REMARK 100 THE RCSB ID CODE IS RCSB040811.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 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 : 3913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.730 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.66 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS SUBSTITUTION REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2O7K REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 30% PEG4000, 0.2M MGCL2, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
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 20.66400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.44000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.61400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.44000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.66400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.61400 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1
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 LYS A 5 CD CE NZ REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 LYS A 54 NZ REMARK 470 GLU A 59 CD OE1 OE2 REMARK 470 SER A 71 OG REMARK 470 LYS A 79 NZ REMARK 470 LYS A 86 NZ REMARK 470 LYS A 93 CD CE NZ REMARK 470 GLU A 94 OE1 OE2 REMARK 470 GLU A 98 CD OE1 OE2 REMARK 470 LYS A 102 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 GLU A 16 -30.38 -153.15 REMARK 500 GLU A 47 21.37 -67.58 REMARK 500 ASN A 60 58.03 -142.02 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O7K RELATED DB: PDB REMARK 900 WILD-TYPE S. AUREUS THIOREDOXIN REMARK 900 RELATED ID: 2O85 RELATED DB: PDB REMARK 900 S. AUREUS THIOREDOXIN P31T MUTANT REMARK 900 RELATED ID: 2O87 RELATED DB: PDB REMARK 900 S. AUREUS THIOREDOXIN P31S MUTANT
DBREF 2O89 A 1 104 UNP P0A0K6 THIO_STAAU 1 104
SEQADV 2O89 GLY A -2 UNP P0A0K6 CLONING ARTIFACT SEQADV 2O89 SER A -1 UNP P0A0K6 CLONING ARTIFACT SEQADV 2O89 HIS A 0 UNP P0A0K6 CLONING ARTIFACT SEQADV 2O89 THR A 31 UNP P0A0K6 PRO 31 ENGINEERED SEQADV 2O89 SER A 32 UNP P0A0K6 CYS 32 ENGINEERED
SEQRES 1 A 107 GLY SER HIS MET ALA ILE VAL LYS VAL THR ASP ALA ASP SEQRES 2 A 107 PHE ASP SER LYS VAL GLU SER GLY VAL GLN LEU VAL ASP SEQRES 3 A 107 PHE TRP ALA THR TRP CYS GLY THR SER LYS MET ILE ALA SEQRES 4 A 107 PRO VAL LEU GLU GLU LEU ALA ALA ASP TYR GLU GLY LYS SEQRES 5 A 107 ALA ASP ILE LEU LYS LEU ASP VAL ASP GLU ASN PRO SER SEQRES 6 A 107 THR ALA ALA LYS TYR GLU VAL MET SER ILE PRO THR LEU SEQRES 7 A 107 ILE VAL PHE LYS ASP GLY GLN PRO VAL ASP LYS VAL VAL SEQRES 8 A 107 GLY PHE GLN PRO LYS GLU ASN LEU ALA GLU VAL LEU ASP SEQRES 9 A 107 LYS HIS LEU
HELIX 1 1 ASP A 10 VAL A 15 1 6 HELIX 2 2 CYS A 29 TYR A 46 1 18 HELIX 3 3 ASN A 60 TYR A 67 1 8 HELIX 4 4 PRO A 92 LYS A 102 1 11
SHEET 1 A 5 VAL A 4 LYS A 5 0 SHEET 2 A 5 ASP A 51 ASP A 56 1 O LYS A 54 N VAL A 4 SHEET 3 A 5 VAL A 19 TRP A 25 1 N ASP A 23 O LEU A 53 SHEET 4 A 5 THR A 74 LYS A 79 -1 O PHE A 78 N GLN A 20 SHEET 5 A 5 GLN A 82 VAL A 88 -1 O VAL A 87 N LEU A 75
CISPEP 1 ILE A 72 PRO A 73 0 0.21
CRYST1 41.328 49.228 54.880 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 0.024197 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020314 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018222 0.00000