HEADER DNA BINDING PROTEIN 08-SEP-21 7VE4 TITLE C-TERMINAL DOMAIN OF VRAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING RESPONSE REGULATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: BSZ10_05280; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TWO-COMPONENT SYSTEM, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.V.KUMAR,C.CHEN,C.H.HSU REVDAT 2 29-NOV-23 7VE4 1 REMARK REVDAT 1 18-MAY-22 7VE4 0 JRNL AUTH J.V.KUMAR,T.S.TSENG,Y.C.LOU,S.Y.WEI,T.H.WU,H.C.TANG, JRNL AUTH 2 Y.C.CHIU,C.H.HSU,C.CHEN JRNL TITL STRUCTURAL INSIGHTS INTO DNA BINDING DOMAIN OF JRNL TITL 2 VANCOMYCIN-RESISTANCE-ASSOCIATED RESPONSE REGULATOR IN JRNL TITL 3 COMPLEX WITH ITS PROMOTER DNA FROM STAPHYLOCOCCUS AUREUS. JRNL REF PROTEIN SCI. V. 31 E4286 2022 JRNL REFN ESSN 1469-896X JRNL PMID 35481641 JRNL DOI 10.1002/PRO.4286 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 9738 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 966 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 24.3090 - 3.5737 0.99 1284 144 0.1491 0.1690 REMARK 3 2 3.5737 - 2.8380 1.00 1275 135 0.1666 0.1896 REMARK 3 3 2.8380 - 2.4796 1.00 1287 141 0.1530 0.1683 REMARK 3 4 2.4796 - 2.2531 1.00 1267 135 0.1624 0.2156 REMARK 3 5 2.2531 - 2.0917 1.00 1263 146 0.1590 0.1753 REMARK 3 6 2.0917 - 1.9684 1.00 1254 136 0.1778 0.2138 REMARK 3 7 1.9684 - 1.8700 0.90 1146 129 0.2187 0.2440 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.23 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 176 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1093 -11.0194 -4.1029 REMARK 3 T TENSOR REMARK 3 T11: 0.1591 T22: 0.3505 REMARK 3 T33: 0.2004 T12: 0.0067 REMARK 3 T13: -0.0599 T23: -0.1309 REMARK 3 L TENSOR REMARK 3 L11: 4.0421 L22: 1.8332 REMARK 3 L33: 1.8634 L12: -0.4822 REMARK 3 L13: -2.2488 L23: -0.0935 REMARK 3 S TENSOR REMARK 3 S11: -0.1013 S12: 0.1678 S13: 0.0591 REMARK 3 S21: -0.2071 S22: -0.2249 S23: 0.3351 REMARK 3 S31: 0.0150 S32: -0.6092 S33: 0.2457 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 209 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4146 -4.0290 7.5205 REMARK 3 T TENSOR REMARK 3 T11: 0.0733 T22: 0.1080 REMARK 3 T33: 0.0951 T12: -0.0401 REMARK 3 T13: -0.0077 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 3.7886 L22: 3.6573 REMARK 3 L33: 4.8318 L12: -0.2379 REMARK 3 L13: -0.3941 L23: 0.3476 REMARK 3 S TENSOR REMARK 3 S11: 0.0859 S12: -0.0715 S13: 0.0115 REMARK 3 S21: 0.1354 S22: -0.1367 S23: 0.0802 REMARK 3 S31: 0.0101 S32: -0.2088 S33: 0.0387 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1538 -14.1910 8.6663 REMARK 3 T TENSOR REMARK 3 T11: 0.2585 T22: 0.3207 REMARK 3 T33: 0.2939 T12: -0.1898 REMARK 3 T13: 0.0703 T23: -0.0885 REMARK 3 L TENSOR REMARK 3 L11: 3.6028 L22: 1.3327 REMARK 3 L33: 0.4902 L12: 0.4317 REMARK 3 L13: -0.6113 L23: -0.2980 REMARK 3 S TENSOR REMARK 3 S11: -0.0407 S12: 0.0663 S13: -0.0977 REMARK 3 S21: 0.0079 S22: -0.0281 S23: 0.1609 REMARK 3 S31: 0.0729 S32: -0.0982 S33: 0.0869 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 161 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3266 -13.5641 3.4856 REMARK 3 T TENSOR REMARK 3 T11: 0.1514 T22: 0.1252 REMARK 3 T33: 0.2007 T12: 0.0054 REMARK 3 T13: -0.0028 T23: -0.0438 REMARK 3 L TENSOR REMARK 3 L11: 2.4495 L22: 5.6870 REMARK 3 L33: 6.4904 L12: 3.0806 REMARK 3 L13: 0.1184 L23: 0.0766 REMARK 3 S TENSOR REMARK 3 S11: 0.0871 S12: 0.0193 S13: -0.7249 REMARK 3 S21: 0.0961 S22: -0.1333 S23: -0.3267 REMARK 3 S31: 0.7262 S32: 0.0032 S33: 0.0336 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 162 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.0349 -13.2217 -5.0123 REMARK 3 T TENSOR REMARK 3 T11: 0.2424 T22: 0.1912 REMARK 3 T33: 0.1674 T12: 0.0337 REMARK 3 T13: 0.0351 T23: -0.0390 REMARK 3 L TENSOR REMARK 3 L11: 1.7167 L22: 5.9306 REMARK 3 L33: 5.1531 L12: 1.6690 REMARK 3 L13: 0.2408 L23: 3.8507 REMARK 3 S TENSOR REMARK 3 S11: 0.0989 S12: -0.1581 S13: -0.0915 REMARK 3 S21: 0.1969 S22: 0.1035 S23: -0.3572 REMARK 3 S31: 0.2497 S32: 0.3389 S33: -0.1812 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 7VE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300023175. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-20 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 : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9739 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 24.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 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: PHASER REMARK 200 STARTING MODEL: 4IF4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH 8.5, 16% PEG 4000 REMARK 280 (W/V), 200 MM MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 27.02100 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 54.04200 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 0.00000 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 27.02100 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 54.04200 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 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 138 REMARK 465 LYS A 139 REMARK 465 LYS A 140 REMARK 465 ARG A 141 DBREF1 7VE4 A 138 209 UNP A0A1Q8DEZ3_STAAU DBREF2 7VE4 A A0A1Q8DEZ3 138 209 SEQRES 1 A 72 MET LYS LYS ARG ALA GLU LEU TYR GLU MET LEU THR GLU SEQRES 2 A 72 ARG GLU MET GLU ILE LEU LEU LEU ILE ALA LYS GLY TYR SEQRES 3 A 72 SER ASN GLN GLU ILE ALA SER ALA SER HIS ILE THR ILE SEQRES 4 A 72 LYS THR VAL LYS THR HIS VAL SER ASN ILE LEU SER LYS SEQRES 5 A 72 LEU GLU VAL GLN ASP ARG THR GLN ALA VAL ILE TYR ALA SEQRES 6 A 72 PHE GLN HIS ASN LEU ILE GLN FORMUL 2 HOH *121(H2 O) HELIX 1 AA1 GLU A 143 LEU A 148 5 6 HELIX 2 AA2 THR A 149 ALA A 160 1 12 HELIX 3 AA3 SER A 164 HIS A 173 1 10 HELIX 4 AA4 THR A 175 GLU A 191 1 17 HELIX 5 AA5 ASP A 194 HIS A 205 1 12 CRYST1 50.963 50.963 81.063 90.00 90.00 120.00 P 64 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 0.019622 0.011329 0.000000 0.00000 SCALE2 0.000000 0.022658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012336 0.00000