HEADER TRANSCRIPTION 29-NOV-17 5YWJ TITLE GLOBAL REGULATORY ELEMENT SARX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR SARX; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STAPHYLOCOCCAL ACCESSORY REGULATOR X; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325); SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325; SOURCE 5 GENE: SARX, SAOUHSC_00674; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS GLOBAL REGULATORY ELEMENT, DNA-BINDING, TRANSCRIPTIONAL CONTRAL, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Q.WANG REVDAT 2 22-NOV-23 5YWJ 1 REMARK REVDAT 1 05-DEC-18 5YWJ 0 JRNL AUTH Q.WANG JRNL TITL CRYSTAL STRUCTURE OF SARX FROM STAPHYLOCOCCUS AUREUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 8323 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 386 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 23.6132 - 3.0299 0.97 2747 127 0.2369 0.2658 REMARK 3 2 3.0299 - 2.4056 1.00 2612 129 0.2947 0.3374 REMARK 3 3 2.4056 - 2.1018 1.00 2578 130 0.2221 0.3035 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.580 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 : 0.007 830 REMARK 3 ANGLE : 1.031 1123 REMARK 3 CHIRALITY : 0.074 140 REMARK 3 PLANARITY : 0.003 137 REMARK 3 DIHEDRAL : 12.939 289 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.0315 10.4895 16.1537 REMARK 3 T TENSOR REMARK 3 T11: 0.2788 T22: 0.2124 REMARK 3 T33: 0.2569 T12: -0.0418 REMARK 3 T13: -0.0117 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 2.7504 L22: 3.7638 REMARK 3 L33: 8.3851 L12: 0.1817 REMARK 3 L13: -1.4917 L23: -2.6501 REMARK 3 S TENSOR REMARK 3 S11: 0.0772 S12: -0.0669 S13: -0.0288 REMARK 3 S21: 0.4889 S22: -0.1017 S23: 0.1421 REMARK 3 S31: -0.3483 S32: 0.2451 S33: 0.0238 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 5YWJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8345 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 57.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 8.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.22100 REMARK 200 R SYM FOR SHELL (I) : 0.22100 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: MOLREP REMARK 200 STARTING MODEL: 5HS5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BICINE PH9.0, 1,4-DIOXANE, PEG 20000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.16K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 115.46500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 16.69600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 16.69600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.73250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 16.69600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 16.69600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 173.19750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 16.69600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.69600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.73250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 16.69600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 16.69600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 173.19750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 115.46500 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 GLU A 7 REMARK 465 THR A 8 REMARK 465 ILE A 119 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 LEU A 9 CG CD1 CD2 REMARK 470 LEU A 10 CG CD1 CD2 REMARK 470 PHE A 12 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 15 CG CD OE1 NE2 REMARK 470 LYS A 17 CG CD CE NZ REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 ASP A 46 CG OD1 OD2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 GLN A 52 CG CD OE1 NE2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 ASP A 60 CG OD1 OD2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 ARG A 66 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 ASP A 90 CG OD1 OD2 REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 ARG A 92 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 ASN A 118 CG OD1 ND2 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 46 -72.33 -83.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YWJ A 1 119 UNP Q2G0D1 SARX_STAA8 1 119 SEQADV 5YWJ HIS A -5 UNP Q2G0D1 EXPRESSION TAG SEQADV 5YWJ HIS A -4 UNP Q2G0D1 EXPRESSION TAG SEQADV 5YWJ HIS A -3 UNP Q2G0D1 EXPRESSION TAG SEQADV 5YWJ HIS A -2 UNP Q2G0D1 EXPRESSION TAG SEQADV 5YWJ HIS A -1 UNP Q2G0D1 EXPRESSION TAG SEQADV 5YWJ HIS A 0 UNP Q2G0D1 EXPRESSION TAG SEQRES 1 A 125 HIS HIS HIS HIS HIS HIS MET ASN THR GLU LYS LEU GLU SEQRES 2 A 125 THR LEU LEU GLY PHE TYR LYS GLN TYR LYS ALA LEU SER SEQRES 3 A 125 GLU TYR ILE ASP LYS LYS TYR LYS LEU SER LEU ASN ASP SEQRES 4 A 125 LEU ALA VAL LEU ASP LEU THR MET LYS HIS CYS LYS ASP SEQRES 5 A 125 GLU LYS VAL LEU MET GLN SER PHE LEU LYS THR ALA MET SEQRES 6 A 125 ASP GLU LEU ASP LEU SER ARG THR LYS LEU LEU VAL SER SEQRES 7 A 125 ILE ARG ARG LEU ILE GLU LYS GLU ARG LEU SER LYS VAL SEQRES 8 A 125 ARG SER SER LYS ASP GLU ARG LYS ILE TYR ILE TYR LEU SEQRES 9 A 125 ASN ASN ASP ASP ILE SER LYS PHE ASN ALA LEU PHE GLU SEQRES 10 A 125 ASP VAL GLU GLN PHE LEU ASN ILE FORMUL 2 HOH *17(H2 O) HELIX 1 AA1 LEU A 9 LYS A 28 1 20 HELIX 2 AA2 SER A 30 CYS A 44 1 15 HELIX 3 AA3 MET A 51 ASP A 63 1 13 HELIX 4 AA4 SER A 65 LYS A 79 1 15 HELIX 5 AA5 ASN A 99 ASN A 118 1 20 SHEET 1 AA1 3 VAL A 49 LEU A 50 0 SHEET 2 AA1 3 ILE A 94 TYR A 97 -1 O ILE A 96 N VAL A 49 SHEET 3 AA1 3 SER A 83 ARG A 86 -1 N VAL A 85 O TYR A 95 CRYST1 33.392 33.392 230.930 90.00 90.00 90.00 P 41 21 2 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 0.029947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029947 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004330 0.00000