HEADER TRANSCRIPTION 11-JUN-19 6K8E TITLE GLOBAL REGULATORY ELEMENT SARX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR SARX; COMPND 3 CHAIN: A, D; 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 GENE: SARX, SAOUHSC_00674; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS GLOBAL REGULATORY ELEMENT, DNA-BINDING, TRANSCRIPTIONAL CONTRAL, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Q.WANG REVDAT 2 22-NOV-23 6K8E 1 REMARK REVDAT 1 17-JUN-20 6K8E 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 856 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 33.4096 - 3.6366 1.00 2682 140 0.1841 0.2218 REMARK 3 2 3.6366 - 2.8870 1.00 2693 146 0.2340 0.2829 REMARK 3 3 2.8870 - 2.5222 1.00 2655 159 0.2560 0.2992 REMARK 3 4 2.5222 - 2.2916 1.00 2696 132 0.2595 0.3462 REMARK 3 5 2.2916 - 2.1274 1.00 2670 134 0.2483 0.3211 REMARK 3 6 2.1274 - 2.0020 1.00 2688 145 0.2484 0.3073 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.010 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 1913 REMARK 3 ANGLE : 0.976 2554 REMARK 3 CHIRALITY : 0.072 293 REMARK 3 PLANARITY : 0.003 314 REMARK 3 DIHEDRAL : 13.878 758 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): -4.2534 12.4363 16.9006 REMARK 3 T TENSOR REMARK 3 T11: 0.2688 T22: 0.2964 REMARK 3 T33: 0.3915 T12: 0.0109 REMARK 3 T13: 0.0024 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.8039 L22: 0.9714 REMARK 3 L33: 8.3773 L12: 0.2333 REMARK 3 L13: 0.9199 L23: -0.9181 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: 0.1795 S13: -0.0975 REMARK 3 S21: 0.1635 S22: -0.0095 S23: 0.0758 REMARK 3 S31: -0.3741 S32: 0.3513 S33: 0.0279 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 6K8E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-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 PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17045 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 FOR THE DATA SET : 19.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : 0.59700 REMARK 200 FOR SHELL : 6.900 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 (%): 41.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE PH 9.0, 2% 1,4-DIOXANE, REMARK 280 10% PEG 20000, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 115.50300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.75150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 173.25450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 GLY A -1 REMARK 465 SER 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 ILE A 119 REMARK 465 HIS D -8 REMARK 465 HIS D -7 REMARK 465 HIS D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 MET D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 MET D 1 REMARK 465 ASN D 2 REMARK 465 THR D 3 REMARK 465 GLU D 4 REMARK 465 ILE D 119 DBREF 6K8E A 1 119 UNP Q2G0D1 SARX_STAA8 1 119 DBREF 6K8E D 1 119 UNP Q2G0D1 SARX_STAA8 1 119 SEQADV 6K8E HIS A -8 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS A -7 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS A -6 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS A -5 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS A -4 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS A -3 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E MET A -2 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E GLY A -1 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E SER A 0 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS D -8 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS D -7 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS D -6 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS D -5 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS D -4 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E HIS D -3 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E MET D -2 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E GLY D -1 UNP Q2G0D1 EXPRESSION TAG SEQADV 6K8E SER D 0 UNP Q2G0D1 EXPRESSION TAG SEQRES 1 A 128 HIS HIS HIS HIS HIS HIS MET GLY SER MET ASN THR GLU SEQRES 2 A 128 LYS LEU GLU THR LEU LEU GLY PHE TYR LYS GLN TYR LYS SEQRES 3 A 128 ALA LEU SER GLU TYR ILE ASP LYS LYS TYR LYS LEU SER SEQRES 4 A 128 LEU ASN ASP LEU ALA VAL LEU ASP LEU THR MET LYS HIS SEQRES 5 A 128 CYS LYS ASP GLU LYS VAL LEU MET GLN SER PHE LEU LYS SEQRES 6 A 128 THR ALA MET ASP GLU LEU ASP LEU SER ARG THR LYS LEU SEQRES 7 A 128 LEU VAL SER ILE ARG ARG LEU ILE GLU LYS GLU ARG LEU SEQRES 8 A 128 SER LYS VAL ARG SER SER LYS ASP GLU ARG LYS ILE TYR SEQRES 9 A 128 ILE TYR LEU ASN ASN ASP ASP ILE SER LYS PHE ASN ALA SEQRES 10 A 128 LEU PHE GLU ASP VAL GLU GLN PHE LEU ASN ILE SEQRES 1 D 128 HIS HIS HIS HIS HIS HIS MET GLY SER MET ASN THR GLU SEQRES 2 D 128 LYS LEU GLU THR LEU LEU GLY PHE TYR LYS GLN TYR LYS SEQRES 3 D 128 ALA LEU SER GLU TYR ILE ASP LYS LYS TYR LYS LEU SER SEQRES 4 D 128 LEU ASN ASP LEU ALA VAL LEU ASP LEU THR MET LYS HIS SEQRES 5 D 128 CYS LYS ASP GLU LYS VAL LEU MET GLN SER PHE LEU LYS SEQRES 6 D 128 THR ALA MET ASP GLU LEU ASP LEU SER ARG THR LYS LEU SEQRES 7 D 128 LEU VAL SER ILE ARG ARG LEU ILE GLU LYS GLU ARG LEU SEQRES 8 D 128 SER LYS VAL ARG SER SER LYS ASP GLU ARG LYS ILE TYR SEQRES 9 D 128 ILE TYR LEU ASN ASN ASP ASP ILE SER LYS PHE ASN ALA SEQRES 10 D 128 LEU PHE GLU ASP VAL GLU GLN PHE LEU ASN ILE FORMUL 3 HOH *53(H2 O) HELIX 1 AA1 THR A 8 LYS A 28 1 21 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 HELIX 6 AA6 LEU D 6 LYS D 28 1 23 HELIX 7 AA7 SER D 30 CYS D 44 1 15 HELIX 8 AA8 MET D 51 ASP D 63 1 13 HELIX 9 AA9 SER D 65 LYS D 79 1 15 HELIX 10 AB1 ASN D 99 LEU D 117 1 19 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 SHEET 1 AA2 3 VAL D 49 LEU D 50 0 SHEET 2 AA2 3 ILE D 94 TYR D 97 -1 O ILE D 96 N VAL D 49 SHEET 3 AA2 3 SER D 83 ARG D 86 -1 N VAL D 85 O TYR D 95 CRYST1 33.405 33.405 231.006 90.00 90.00 90.00 P 41 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 0.029936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004329 0.00000