HEADER DNA BINDING PROTEIN 16-JUL-12 4G4K TITLE STRUCTURE OF THE STAPHYLOCOCCUS AUREUS AGRA LYTTR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACCESSORY GENE REGULATOR PROTEIN A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: AGRA LYTTR DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: AGR, AGRA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET9A KEYWDS AGRA, RESPONSE REGULATOR, ACTIVATOR, TRANSCRIPTION FACTOR, KEYWDS 2 PHOSPHOPROTEIN, TRANSCRIPTION REGULATION, TWO-COMPONENT SYSTEM, KEYWDS 3 LYTTR DOMAIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.G.LEONARD,I.F.BEZAR,A.M.STOCK REVDAT 3 13-SEP-23 4G4K 1 REMARK SEQADV REVDAT 2 02-JAN-13 4G4K 1 JRNL REVDAT 1 19-DEC-12 4G4K 0 JRNL AUTH P.G.LEONARD,I.F.BEZAR,D.J.SIDOTE,A.M.STOCK JRNL TITL IDENTIFICATION OF A HYDROPHOBIC CLEFT IN THE LYTTR DOMAIN OF JRNL TITL 2 AGRA AS A LOCUS FOR SMALL MOLECULE INTERACTIONS THAT INHIBIT JRNL TITL 3 DNA BINDING. JRNL REF BIOCHEMISTRY V. 51 10035 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 23181972 JRNL DOI 10.1021/BI3011785 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1066 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 31964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1600 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 20.7178 - 3.3760 0.99 3076 161 0.1657 0.1899 REMARK 3 2 3.3760 - 2.6815 1.00 2947 155 0.1791 0.2065 REMARK 3 3 2.6815 - 2.3431 0.99 2913 153 0.1858 0.1931 REMARK 3 4 2.3431 - 2.1291 0.98 2845 150 0.1713 0.1915 REMARK 3 5 2.1291 - 1.9766 0.98 2815 149 0.1661 0.2492 REMARK 3 6 1.9766 - 1.8601 0.96 2785 147 0.1754 0.2187 REMARK 3 7 1.8601 - 1.7670 0.95 2717 146 0.1818 0.2084 REMARK 3 8 1.7670 - 1.6901 0.93 2709 142 0.1948 0.2308 REMARK 3 9 1.6901 - 1.6251 0.92 2637 145 0.2129 0.2310 REMARK 3 10 1.6251 - 1.5690 0.89 2573 136 0.2420 0.2681 REMARK 3 11 1.5690 - 1.5200 0.82 2347 116 0.3159 0.3638 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.16 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 : 0.006 1755 REMARK 3 ANGLE : 1.048 2357 REMARK 3 CHIRALITY : 0.083 248 REMARK 3 PLANARITY : 0.004 306 REMARK 3 DIHEDRAL : 13.135 676 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 4G4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX HR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56300 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, RESOLVE REMARK 200 STARTING MODEL: PDB ENTRY 3BS1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 150 MM LISO4, 11% (W/V) REMARK 280 PEG 4000, PH 8.0, VAPOR DIFFUSION, HANGING 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 20.70700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.06900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.94700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.06900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.70700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.94700 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 MET A 136 REMARK 465 ASP A 137 REMARK 465 ASN A 138 REMARK 465 SER A 139 REMARK 465 VAL A 140 REMARK 465 MET B 136 REMARK 465 ASP B 137 REMARK 465 ASN B 138 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 LYS A 225 -4.29 80.05 REMARK 500 ARG B 147 57.87 -151.43 REMARK 500 LYS B 225 -1.67 74.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BS1 RELATED DB: PDB REMARK 900 AGRA LYTTR DOMAIN BOUND TO DNA DUPLEX DBREF 4G4K A 137 238 UNP P0A0I7 AGRA_STAAU 137 238 DBREF 4G4K B 137 238 UNP P0A0I7 AGRA_STAAU 137 238 SEQADV 4G4K MET A 136 UNP P0A0I7 INITIATING METHIONINE SEQADV 4G4K MET B 136 UNP P0A0I7 INITIATING METHIONINE SEQRES 1 A 103 MET ASP ASN SER VAL GLU THR ILE GLU LEU LYS ARG GLY SEQRES 2 A 103 SER ASN SER VAL TYR VAL GLN TYR ASP ASP ILE MET PHE SEQRES 3 A 103 PHE GLU SER SER THR LYS SER HIS ARG LEU ILE ALA HIS SEQRES 4 A 103 LEU ASP ASN ARG GLN ILE GLU PHE TYR GLY ASN LEU LYS SEQRES 5 A 103 GLU LEU SER GLN LEU ASP ASP ARG PHE PHE ARG CYS HIS SEQRES 6 A 103 ASN SER PHE VAL VAL ASN ARG HIS ASN ILE GLU SER ILE SEQRES 7 A 103 ASP SER LYS GLU ARG ILE VAL TYR PHE LYS ASN LYS GLU SEQRES 8 A 103 HIS CYS TYR ALA SER VAL ARG ASN VAL LYS LYS ILE SEQRES 1 B 103 MET ASP ASN SER VAL GLU THR ILE GLU LEU LYS ARG GLY SEQRES 2 B 103 SER ASN SER VAL TYR VAL GLN TYR ASP ASP ILE MET PHE SEQRES 3 B 103 PHE GLU SER SER THR LYS SER HIS ARG LEU ILE ALA HIS SEQRES 4 B 103 LEU ASP ASN ARG GLN ILE GLU PHE TYR GLY ASN LEU LYS SEQRES 5 B 103 GLU LEU SER GLN LEU ASP ASP ARG PHE PHE ARG CYS HIS SEQRES 6 B 103 ASN SER PHE VAL VAL ASN ARG HIS ASN ILE GLU SER ILE SEQRES 7 B 103 ASP SER LYS GLU ARG ILE VAL TYR PHE LYS ASN LYS GLU SEQRES 8 B 103 HIS CYS TYR ALA SER VAL ARG ASN VAL LYS LYS ILE HET GOL A 301 6 HET GOL A 302 6 HET GOL B 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 HOH *254(H2 O) HELIX 1 1 ASN A 185 GLN A 191 1 7 HELIX 2 2 ASN A 234 ILE A 238 5 5 HELIX 3 3 ASN B 185 GLN B 191 1 7 HELIX 4 4 ASN B 234 ILE B 238 5 5 SHEET 1 A 2 THR A 142 LYS A 146 0 SHEET 2 A 2 SER A 151 GLN A 155 -1 O VAL A 152 N LEU A 145 SHEET 1 B 5 GLN A 179 PHE A 182 0 SHEET 2 B 5 LEU A 171 LEU A 175 -1 N ALA A 173 O ILE A 180 SHEET 3 B 5 ILE A 159 GLU A 163 -1 N MET A 160 O HIS A 174 SHEET 4 B 5 PHE A 203 ASN A 206 -1 O VAL A 204 N PHE A 162 SHEET 5 B 5 PHE A 196 HIS A 200 -1 N PHE A 197 O VAL A 205 SHEET 1 C 3 ILE A 210 ASP A 214 0 SHEET 2 C 3 ILE A 219 PHE A 222 -1 O TYR A 221 N GLU A 211 SHEET 3 C 3 HIS A 227 TYR A 229 -1 O CYS A 228 N VAL A 220 SHEET 1 D 2 THR B 142 LEU B 145 0 SHEET 2 D 2 VAL B 152 GLN B 155 -1 O VAL B 154 N ILE B 143 SHEET 1 E 5 GLN B 179 PHE B 182 0 SHEET 2 E 5 LEU B 171 LEU B 175 -1 N ALA B 173 O ILE B 180 SHEET 3 E 5 ILE B 159 SER B 164 -1 N MET B 160 O HIS B 174 SHEET 4 E 5 PHE B 203 ASN B 206 -1 O VAL B 204 N PHE B 162 SHEET 5 E 5 PHE B 196 HIS B 200 -1 N PHE B 197 O VAL B 205 SHEET 1 F 3 ILE B 210 ASP B 214 0 SHEET 2 F 3 ILE B 219 PHE B 222 -1 O TYR B 221 N GLU B 211 SHEET 3 F 3 HIS B 227 TYR B 229 -1 O CYS B 228 N VAL B 220 SITE 1 AC1 7 HIS A 200 ARG A 218 HOH A 402 HOH A 483 SITE 2 AC1 7 HOH A 550 ASN B 177 ARG B 178 SITE 1 AC2 3 ARG A 178 HIS B 200 HOH B 448 SITE 1 AC3 9 ARG A 207 LYS A 225 ILE A 238 HOH A 452 SITE 2 AC3 9 GLU B 144 LYS B 146 TYR B 153 HOH B 406 SITE 3 AC3 9 HOH B 410 CRYST1 41.414 45.894 112.138 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 0.024146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008918 0.00000