HEADER DNA BINDING PROTEIN 01-AUG-14 4U88 TITLE STRUCTURE OF THE DNA-BINDING DOMAIN OF THE RESPONSE REGULATOR SAER TITLE 2 FROM STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR SAER; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 128-228; COMPND 5 SYNONYM: SAER; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS USA300-ISMMS1; SOURCE 3 ORGANISM_TAXID: 1458279; SOURCE 4 GENE: AZ30_03680; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DNA-BINDING PROTEIN, TRANSCRIPTIONAL, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.S.LIU,C.H.HUANG,C.S.YANG,S.C.CHEN,Y.CHEN REVDAT 2 08-NOV-23 4U88 1 REMARK REVDAT 1 12-AUG-15 4U88 0 JRNL AUTH J.S.LIU,C.H.HUANG,C.S.YANG,S.C.CHEN,Y.CHEN JRNL TITL STRUCTURE OF THE DNA-BINDING DOMAIN OF THE RESPONSE JRNL TITL 2 REGULATOR SAER FROM STAPHYLOCOCCUS AUREUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 9951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 996 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 29.5230 - 4.4995 1.00 1382 155 0.1708 0.2305 REMARK 3 2 4.4995 - 3.5733 1.00 1291 143 0.1675 0.2174 REMARK 3 3 3.5733 - 3.1222 1.00 1295 143 0.2131 0.2920 REMARK 3 4 3.1222 - 2.8370 1.00 1267 141 0.2186 0.3179 REMARK 3 5 2.8370 - 2.6338 1.00 1258 141 0.2277 0.3135 REMARK 3 6 2.6338 - 2.4786 1.00 1245 137 0.2278 0.3073 REMARK 3 7 2.4786 - 2.3545 0.96 1217 136 0.2535 0.3632 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.020 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 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 : 0.009 1649 REMARK 3 ANGLE : 1.163 2230 REMARK 3 CHIRALITY : 0.046 253 REMARK 3 PLANARITY : 0.006 273 REMARK 3 DIHEDRAL : 13.259 604 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 4U88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000202973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9992 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 STARTING MODEL: 4IXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% V/V TACSIMATE, PH 7.0, 0.1M HEPES REMARK 280 PH 7.0, 10% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 15.98300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.37950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.51200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.37950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.98300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.51200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 136 REMARK 465 TYR A 137 REMARK 465 ASP A 138 REMARK 465 TYR A 139 REMARK 465 TYR A 140 REMARK 465 GLU A 141 REMARK 465 ASP A 142 REMARK 465 ARG 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 465 SER B 180 REMARK 465 ARG B 181 REMARK 465 LEU B 182 REMARK 465 GLU B 183 REMARK 465 HIS B 184 REMARK 465 HIS B 185 REMARK 465 HIS B 186 REMARK 465 HIS B 187 REMARK 465 HIS B 188 REMARK 465 HIS B 189 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU B 112 O HOH B 204 2.02 REMARK 500 NE ARG A 120 O HOH A 210 2.11 REMARK 500 OG1 THR B 89 O HOH B 201 2.14 REMARK 500 NH1 ARG A 107 OE2 GLU A 110 2.19 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 ASP A 86 -128.98 53.74 REMARK 500 ASN A 122 -7.58 74.42 REMARK 500 ASP B 86 -130.30 53.37 REMARK 500 ASN B 122 -6.34 72.54 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 B 211 DISTANCE = 6.07 ANGSTROMS DBREF 4U88 A 81 181 UNP W6DZ35 W6DZ35_STAAU 128 228 DBREF 4U88 B 81 181 UNP W6DZ35 W6DZ35_STAAU 128 228 SEQADV 4U88 LEU A 182 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 GLU A 183 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS A 184 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS A 185 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS A 186 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS A 187 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS A 188 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS A 189 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 LEU B 182 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 GLU B 183 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS B 184 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS B 185 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS B 186 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS B 187 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS B 188 UNP W6DZ35 EXPRESSION TAG SEQADV 4U88 HIS B 189 UNP W6DZ35 EXPRESSION TAG SEQRES 1 A 109 GLU GLN LEU SER PHE ASP GLU LEU THR LEU ILE ASN LEU SEQRES 2 A 109 SER LYS VAL VAL THR VAL ASN GLY HIS GLU VAL PRO MET SEQRES 3 A 109 ARG ILE LYS GLU PHE GLU LEU LEU TRP TYR LEU ALA SER SEQRES 4 A 109 ARG GLU ASN GLU VAL ILE SER LYS SER GLU LEU LEU GLU SEQRES 5 A 109 LYS VAL TRP GLY TYR ASP TYR TYR GLU ASP ALA ASN THR SEQRES 6 A 109 VAL ASN VAL HIS ILE HIS ARG ILE ARG GLU LYS LEU GLU SEQRES 7 A 109 LYS GLU SER PHE THR THR TYR THR ILE THR THR VAL TRP SEQRES 8 A 109 GLY LEU GLY TYR LYS PHE GLU ARG SER ARG LEU GLU HIS SEQRES 9 A 109 HIS HIS HIS HIS HIS SEQRES 1 B 109 GLU GLN LEU SER PHE ASP GLU LEU THR LEU ILE ASN LEU SEQRES 2 B 109 SER LYS VAL VAL THR VAL ASN GLY HIS GLU VAL PRO MET SEQRES 3 B 109 ARG ILE LYS GLU PHE GLU LEU LEU TRP TYR LEU ALA SER SEQRES 4 B 109 ARG GLU ASN GLU VAL ILE SER LYS SER GLU LEU LEU GLU SEQRES 5 B 109 LYS VAL TRP GLY TYR ASP TYR TYR GLU ASP ALA ASN THR SEQRES 6 B 109 VAL ASN VAL HIS ILE HIS ARG ILE ARG GLU LYS LEU GLU SEQRES 7 B 109 LYS GLU SER PHE THR THR TYR THR ILE THR THR VAL TRP SEQRES 8 B 109 GLY LEU GLY TYR LYS PHE GLU ARG SER ARG LEU GLU HIS SEQRES 9 B 109 HIS HIS HIS HIS HIS FORMUL 3 HOH *36(H2 O) HELIX 1 AA1 ARG A 107 SER A 119 1 13 HELIX 2 AA2 SER A 126 TRP A 135 1 10 HELIX 3 AA3 ASN A 144 GLU A 160 1 17 HELIX 4 AA4 ARG B 107 SER B 119 1 13 HELIX 5 AA5 SER B 126 GLY B 136 1 11 HELIX 6 AA6 ALA B 143 GLU B 160 1 18 SHEET 1 AA1 4 GLN A 82 PHE A 85 0 SHEET 2 AA1 4 LEU A 88 ILE A 91 -1 O LEU A 90 N LEU A 83 SHEET 3 AA1 4 VAL A 96 VAL A 99 -1 O THR A 98 N THR A 89 SHEET 4 AA1 4 HIS A 102 GLU A 103 -1 O HIS A 102 N VAL A 99 SHEET 1 AA2 2 TYR A 165 VAL A 170 0 SHEET 2 AA2 2 GLY A 174 ARG A 179 -1 O LYS A 176 N THR A 168 SHEET 1 AA3 4 GLN B 82 PHE B 85 0 SHEET 2 AA3 4 LEU B 88 ILE B 91 -1 O LEU B 90 N LEU B 83 SHEET 3 AA3 4 VAL B 96 VAL B 99 -1 O THR B 98 N THR B 89 SHEET 4 AA3 4 HIS B 102 GLU B 103 -1 O HIS B 102 N VAL B 99 SHEET 1 AA4 2 THR B 166 VAL B 170 0 SHEET 2 AA4 2 GLY B 174 GLU B 178 -1 O GLY B 174 N VAL B 170 CRYST1 31.966 61.024 116.759 90.00 90.00 90.00 P 21 21 21 8 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 0.031283 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008565 0.00000