HEADER TRANSCRIPTION 08-FEB-18 6CDA TITLE CRYSTAL STRUCTURE OF L34A CZRA IN THE ZN(II)BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARSR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CZRA PROTEIN,HTH-TYPE TRANSCRIPTIONAL REPRESSOR CZRA, COMPND 5 PUTATIVE HTH-TYPE TRANSCRIPTIONAL REPRESSOR CZRA,REPRESSOR PROTEIN, COMPND 6 TRANSCRIPTIONAL REGULATOR,ZN(II) OR CO(II)-SPECIFIC TRANSCRIPTIONAL COMPND 7 REPRESSOR PROTEIN; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: RZCA, CZRA, CZRA, AFO97_05125, B9Z04_11610, B9Z08_13310, SOURCE 5 BJI53_13345, BN1321_350009, EP54_06885, EQ90_13065, ERS072738_01903, SOURCE 6 ERS072840_01825, HMPREF3211_00009; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION REGULATOR, ZN-BINDING PROTEIN, DNA BINDING PROTEIN, KEYWDS 2 ARSR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR D.A.CAPDEVILA,G.GONZALEZ-GUTIERREZ,D.P.GIEDROC REVDAT 6 04-OCT-23 6CDA 1 REMARK REVDAT 5 01-JAN-20 6CDA 1 REMARK REVDAT 4 20-FEB-19 6CDA 1 REMARK REVDAT 3 01-AUG-18 6CDA 1 JRNL REVDAT 2 25-JUL-18 6CDA 1 JRNL REVDAT 1 11-JUL-18 6CDA 0 JRNL AUTH D.A.CAPDEVILA,K.A.EDMONDS,G.C.CAMPANELLO,H.WU, JRNL AUTH 2 G.GONZALEZ-GUTIERREZ,D.P.GIEDROC JRNL TITL FUNCTIONAL ROLE OF SOLVENT ENTROPY AND CONFORMATIONAL JRNL TITL 2 ENTROPY OF METAL BINDING IN A DYNAMICALLY DRIVEN ALLOSTERIC JRNL TITL 3 SYSTEM. JRNL REF J. AM. CHEM. SOC. V. 140 9108 2018 JRNL REFN ESSN 1520-5126 JRNL PMID 29953213 JRNL DOI 10.1021/JACS.8B02129 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 45.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 6867 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) : 0.199 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.74 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 : 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 6CDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6867 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 17.6000 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 : 13.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.06900 REMARK 200 FOR SHELL : 2.500 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: 1R1U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE (PH 9) AND REMARK 280 POLYETHYLENE GLYCOL 550 20-22%, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 91.69600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.99350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.99350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.84800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.99350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.99350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 137.54400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.99350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.99350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.84800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.99350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.99350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 137.54400 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 91.69600 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 TYR A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 GLU A 103 REMARK 465 SER A 104 REMARK 465 GLY A 105 REMARK 465 LEU A 106 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HD1 HIS A 97 ZN ZN A 201 7555 1.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 84 OD1 REMARK 620 2 HIS A 86 ND1 110.2 REMARK 620 3 HIS A 97 ND1 120.5 57.8 REMARK 620 4 HIS A 100 NE2 114.8 54.6 6.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 206 DBREF 6CDA A 1 106 UNP O85142 O85142_STAAU 1 106 SEQADV 6CDA ALA A 34 UNP O85142 LEU 34 ENGINEERED MUTATION SEQRES 1 A 106 MET SER GLU GLN TYR SER GLU ILE ASN THR ASP THR LEU SEQRES 2 A 106 GLU ARG VAL THR GLU ILE PHE LYS ALA LEU GLY ASP TYR SEQRES 3 A 106 ASN ARG ILE ARG ILE MET GLU ALA LEU SER VAL SER GLU SEQRES 4 A 106 ALA SER VAL GLY HIS ILE SER HIS GLN LEU ASN LEU SER SEQRES 5 A 106 GLN SER ASN VAL SER HIS GLN LEU LYS LEU LEU LYS SER SEQRES 6 A 106 VAL HIS LEU VAL LYS ALA LYS ARG GLN GLY GLN SER MET SEQRES 7 A 106 ILE TYR SER LEU ASP ASP ILE HIS VAL ALA THR MET LEU SEQRES 8 A 106 LYS GLN ALA ILE HIS HIS ALA ASN HIS PRO LYS GLU SER SEQRES 9 A 106 GLY LEU HET ZN A 201 1 HET CL A 202 1 HET CL A 203 1 HET PG4 A 204 31 HET GOL A 205 14 HET GOL A 206 14 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 CL 2(CL 1-) FORMUL 5 PG4 C8 H18 O5 FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *37(H2 O) HELIX 1 AA1 ASN A 9 GLY A 24 1 16 HELIX 2 AA2 ASP A 25 SER A 38 1 14 HELIX 3 AA3 SER A 41 ASN A 50 1 10 HELIX 4 AA4 SER A 52 VAL A 66 1 15 HELIX 5 AA5 ASP A 84 ASN A 99 1 16 SHEET 1 AA1 2 VAL A 69 GLN A 74 0 SHEET 2 AA1 2 SER A 77 LEU A 82 -1 O ILE A 79 N LYS A 72 LINK OD1 ASP A 84 ZN ZN A 201 1555 1555 2.00 LINK ND1 HIS A 86 ZN ZN A 201 1555 1555 2.07 LINK ND1 HIS A 97 ZN ZN A 201 1555 7555 2.17 LINK NE2 HIS A 100 ZN ZN A 201 1555 7555 1.94 SITE 1 AC1 4 ASP A 84 HIS A 86 HIS A 97 HIS A 100 SITE 1 AC2 5 ALA A 40 SER A 41 HIS A 44 LYS A 61 SITE 2 AC2 5 LYS A 64 SITE 1 AC3 2 GLU A 39 GOL A 206 SITE 1 AC4 13 GLU A 14 ASP A 25 TYR A 26 ASN A 27 SITE 2 AC4 13 ASP A 84 ILE A 85 HIS A 86 HIS A 100 SITE 3 AC4 13 PRO A 101 GOL A 205 HOH A 314 HOH A 320 SITE 4 AC4 13 HOH A 327 SITE 1 AC5 6 GLU A 14 THR A 17 TYR A 26 HIS A 86 SITE 2 AC5 6 HIS A 100 PG4 A 204 SITE 1 AC6 3 GLU A 39 SER A 57 CL A 203 CRYST1 31.987 31.987 183.392 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 0.031263 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005453 0.00000