HEADER OXIDOREDUCTASE 13-NOV-07 3BD2 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS DSBA E96Q COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISULFIDE BOND PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES IN DATABASE 24-199; COMPND 5 SYNONYM: THIOL:DISULFIDE OXIDOREDUCTASE DSBA; 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 STRAIN: BB270; SOURCE 5 GENE: AAG41993; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS THIOL-DISULFIDE OXIDOREDUCTASE, REDOX PROTEIN, PROTEIN FOLDING, REDOX KEYWDS 2 ACTIVE CENTRE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.HERAS,L.THONY-MEYER,J.L.MARTIN REVDAT 6 01-NOV-23 3BD2 1 REMARK REVDAT 5 10-NOV-21 3BD2 1 SEQADV REVDAT 4 25-OCT-17 3BD2 1 REMARK REVDAT 3 24-FEB-09 3BD2 1 VERSN REVDAT 2 11-MAR-08 3BD2 1 JRNL REVDAT 1 11-DEC-07 3BD2 0 JRNL AUTH B.HERAS,M.KURZ,R.JARROTT,S.R.SHOULDICE,P.FREI,G.ROBIN, JRNL AUTH 2 M.CEMAZAR,L.THONY-MEYER,R.GLOCKSHUBER,J.L.MARTIN JRNL TITL STAPHYLOCOCCUS AUREUS DSBA DOES NOT HAVE A DESTABILIZING JRNL TITL 2 DISULFIDE: A NEW PARADIGM FOR BACTERIAL OXIDATIVE FOLDING JRNL REF J.BIOL.CHEM. V. 283 4261 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18077463 JRNL DOI 10.1074/JBC.M707838200 REMARK 2 REMARK 2 RESOLUTION. 1.81 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 23690 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) : 0.243 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2353 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2208 REMARK 3 BIN R VALUE (WORKING SET) : 0.3990 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 244 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1357 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.79900 REMARK 3 B22 (A**2) : -3.79900 REMARK 3 B33 (A**2) : 7.59800 REMARK 3 B12 (A**2) : -2.72400 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC 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 : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 52.95 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL MAXFLUX REMARK 200 OPTICS : OSMIC CONFOCAL MAX-FLUX OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 36.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3BCI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28-30% PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.78933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.89467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.34200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.44733 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.23667 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 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 MET A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 465 SER A 10 REMARK 465 SER A 11 REMARK 465 LYS A 12 REMARK 465 ASN A 13 REMARK 465 ASP A 178 REMARK 465 LYS A 179 REMARK 465 ILE A 180 REMARK 465 LYS A 181 REMARK 465 LEU A 182 REMARK 465 GLU A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 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 TYR A 44 -30.88 -134.83 REMARK 500 LEU A 60 49.64 -106.04 REMARK 500 GLN A 94 -165.01 -119.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BCI RELATED DB: PDB REMARK 900 RELATED ID: 3BCK RELATED DB: PDB REMARK 900 RELATED ID: 1BED RELATED DB: PDB REMARK 900 RELATED ID: 1DSB RELATED DB: PDB DBREF 3BD2 A 6 181 UNP Q9EYL5 Q9EYL5_STAAU 24 199 SEQADV 3BD2 MET A 4 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 ALA A 5 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 GLN A 96 UNP Q9EYL5 GLU 114 ENGINEERED MUTATION SEQADV 3BD2 LEU A 182 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 GLU A 183 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 HIS A 184 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 HIS A 185 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 HIS A 186 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 HIS A 187 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 HIS A 188 UNP Q9EYL5 EXPRESSION TAG SEQADV 3BD2 HIS A 189 UNP Q9EYL5 EXPRESSION TAG SEQRES 1 A 186 MET ALA SER ALA THR THR SER SER LYS ASN GLY LYS PRO SEQRES 2 A 186 LEU VAL VAL VAL TYR GLY ASP TYR LYS CYS PRO TYR CYS SEQRES 3 A 186 LYS GLU LEU ASP GLU LYS VAL MET PRO LYS LEU ARG LYS SEQRES 4 A 186 ASN TYR ILE ASP ASN HIS LYS VAL GLU TYR GLN PHE VAL SEQRES 5 A 186 ASN LEU ALA PHE LEU GLY LYS ASP SER ILE VAL GLY SER SEQRES 6 A 186 ARG ALA SER HIS ALA VAL LEU MET TYR ALA PRO LYS SER SEQRES 7 A 186 PHE LEU ASP PHE GLN LYS GLN LEU PHE ALA ALA GLN GLN SEQRES 8 A 186 ASP GLN ASN LYS GLU TRP LEU THR LYS GLU LEU LEU ASP SEQRES 9 A 186 LYS HIS ILE LYS GLN LEU HIS LEU ASP LYS GLU THR GLU SEQRES 10 A 186 ASN LYS ILE ILE LYS ASP TYR LYS THR LYS ASP SER LYS SEQRES 11 A 186 SER TRP LYS ALA ALA GLU LYS ASP LYS LYS ILE ALA LYS SEQRES 12 A 186 ASP ASN HIS ILE LYS THR THR PRO THR ALA PHE ILE ASN SEQRES 13 A 186 GLY GLU LYS VAL GLU ASP PRO TYR ASP TYR GLU SER TYR SEQRES 14 A 186 GLU LYS LEU LEU LYS ASP LYS ILE LYS LEU GLU HIS HIS SEQRES 15 A 186 HIS HIS HIS HIS FORMUL 2 HOH *225(H2 O) HELIX 1 1 CYS A 26 TYR A 44 1 19 HELIX 2 2 ASP A 63 ALA A 78 1 16 HELIX 3 3 SER A 81 ALA A 92 1 12 HELIX 4 4 THR A 102 GLN A 112 1 11 HELIX 5 5 ASP A 116 THR A 129 1 14 HELIX 6 6 SER A 132 ASN A 148 1 17 HELIX 7 7 ASP A 168 LYS A 177 1 10 SHEET 1 A 4 GLU A 51 ASN A 56 0 SHEET 2 A 4 LEU A 17 GLY A 22 1 N VAL A 18 O GLU A 51 SHEET 3 A 4 THR A 155 ILE A 158 -1 O PHE A 157 N VAL A 19 SHEET 4 A 4 GLU A 161 LYS A 162 -1 O GLU A 161 N ILE A 158 SSBOND 1 CYS A 26 CYS A 29 1555 1555 2.01 CISPEP 1 THR A 153 PRO A 154 0 0.00 CRYST1 72.418 72.418 92.684 90.00 90.00 120.00 P 65 6 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 0.013809 0.007972 0.000000 0.00000 SCALE2 0.000000 0.015945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010789 0.00000