HEADER TRANSCRIPTION 04-NOV-19 6UVU TITLE CRYSTAL STRUCTURE OF THE ANTR ANTIMONY-SPECIFIC TRANSCRIPTIONAL TITLE 2 REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARSR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI; SOURCE 3 ORGANISM_TAXID: 285; SOURCE 4 GENE: P353_26355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ARSR, ARSENIC/ANTIMONY BINDING, TRANSCRIPTIONAL REPRESSOR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR V.THIRUSELVAM,S.BANUMATHI,K.PALANI,R.MANOHAR,B.P.ROSEN REVDAT 4 11-OCT-23 6UVU 1 REMARK REVDAT 3 08-SEP-21 6UVU 1 JRNL REVDAT 2 14-APR-21 6UVU 1 JRNL REVDAT 1 04-NOV-20 6UVU 0 JRNL AUTH T.VISWANATHAN,J.CHEN,M.WU,L.AN,P.KANDAVELU,B.SANKARAN, JRNL AUTH 2 M.RADHAKRISHNAN,M.LI,B.P.ROSEN JRNL TITL FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF ANTR, AN JRNL TITL 2 SB(III) RESPONSIVE TRANSCRIPTIONAL REPRESSOR. JRNL REF MOL.MICROBIOL. V. 116 427 2021 JRNL REFN ESSN 1365-2958 JRNL PMID 33786926 JRNL DOI 10.1111/MMI.14721 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 47.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 16347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 872 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 47.1100 - 3.8200 0.99 2617 184 0.1788 0.2029 REMARK 3 2 3.8200 - 3.0300 1.00 2613 150 0.2151 0.2735 REMARK 3 3 3.0300 - 2.6500 0.99 2576 142 0.2571 0.3452 REMARK 3 4 2.6500 - 2.4000 1.00 2581 166 0.2380 0.3100 REMARK 3 5 2.4000 - 2.2300 0.95 2467 128 0.2983 0.3562 REMARK 3 6 2.2300 - 2.1000 0.99 2621 102 0.2690 0.2983 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) : 0.291 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.063 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.66 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 1713 REMARK 3 ANGLE : 0.950 2312 REMARK 3 CHIRALITY : 0.054 283 REMARK 3 PLANARITY : 0.005 302 REMARK 3 DIHEDRAL : 15.420 1076 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 6UVU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16526 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8700 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) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.620 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: 1SMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM PH 7.5, 10% V/V 2 REMARK 280 -PROPANOL, 20% W/V POLYETHYLENE GLYCOL 4,000, 0.1 M TCEP, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.25500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 ARG A 6 REMARK 465 ASN A 7 REMARK 465 GLU A 8 REMARK 465 LEU A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LEU B 3 REMARK 465 GLU B 4 REMARK 465 LYS B 5 REMARK 465 ARG B 6 REMARK 465 ASN B 7 REMARK 465 GLU B 8 REMARK 465 LEU B 9 REMARK 465 PRO B 10 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 GLN A 121 CG CD OE1 NE2 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 GLN A 120 -3.44 73.09 REMARK 500 CYS B 12 71.46 63.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 261 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B 250 DISTANCE = 7.39 ANGSTROMS DBREF1 6UVU A 1 124 UNP A0A096F4H2_COMTE DBREF2 6UVU A A0A096F4H2 1 124 DBREF1 6UVU B 1 124 UNP A0A096F4H2_COMTE DBREF2 6UVU B A0A096F4H2 1 124 SEQRES 1 A 124 MET ALA LEU GLU LYS ARG ASN GLU LEU PRO ALA CYS SER SEQRES 2 A 124 LEU LYS PRO SER LEU GLN ASP ARG ASP LEU ILE THR SER SEQRES 3 A 124 ALA GLU ALA GLY GLU VAL VAL VAL LEU PHE LYS VAL LEU SEQRES 4 A 124 ALA ASN ASP THR ARG LEU ARG LEU LEU HIS ALA LEU ALA SEQRES 5 A 124 ARG SER GLY GLY LEU CYS VAL THR ASP LEU ALA ALA ALA SEQRES 6 A 124 VAL GLY MET LYS PRO GLN ALA VAL SER ASN GLN LEU GLN SEQRES 7 A 124 ARG LEU ALA ASP ARG ARG ILE LEU ARG ALA ALA ARG CYS SEQRES 8 A 124 GLY ASN ASN ILE HIS TYR ARG ILE VAL ASP PRO CYS VAL SEQRES 9 A 124 LEU ARG MET LEU GLU LEU GLY LEU CYS LEU ILE GLU GLU SEQRES 10 A 124 ALA GLU GLN GLN ALA GLY GLY SEQRES 1 B 124 MET ALA LEU GLU LYS ARG ASN GLU LEU PRO ALA CYS SER SEQRES 2 B 124 LEU LYS PRO SER LEU GLN ASP ARG ASP LEU ILE THR SER SEQRES 3 B 124 ALA GLU ALA GLY GLU VAL VAL VAL LEU PHE LYS VAL LEU SEQRES 4 B 124 ALA ASN ASP THR ARG LEU ARG LEU LEU HIS ALA LEU ALA SEQRES 5 B 124 ARG SER GLY GLY LEU CYS VAL THR ASP LEU ALA ALA ALA SEQRES 6 B 124 VAL GLY MET LYS PRO GLN ALA VAL SER ASN GLN LEU GLN SEQRES 7 B 124 ARG LEU ALA ASP ARG ARG ILE LEU ARG ALA ALA ARG CYS SEQRES 8 B 124 GLY ASN ASN ILE HIS TYR ARG ILE VAL ASP PRO CYS VAL SEQRES 9 B 124 LEU ARG MET LEU GLU LEU GLY LEU CYS LEU ILE GLU GLU SEQRES 10 B 124 ALA GLU GLN GLN ALA GLY GLY FORMUL 3 HOH *111(H2 O) HELIX 1 AA1 LYS A 15 GLN A 19 5 5 HELIX 2 AA2 THR A 25 ALA A 40 1 16 HELIX 3 AA3 ASN A 41 GLY A 55 1 15 HELIX 4 AA4 VAL A 59 VAL A 66 1 8 HELIX 5 AA5 LYS A 69 ARG A 83 1 15 HELIX 6 AA6 ASP A 101 GLU A 119 1 19 HELIX 7 AA7 LYS B 15 GLN B 19 5 5 HELIX 8 AA8 THR B 25 ALA B 40 1 16 HELIX 9 AA9 ASN B 41 GLY B 55 1 15 HELIX 10 AB1 CYS B 58 VAL B 66 1 9 HELIX 11 AB2 LYS B 69 ARG B 83 1 15 HELIX 12 AB3 ASP B 101 ALA B 122 1 22 SHEET 1 AA1 3 LEU A 57 CYS A 58 0 SHEET 2 AA1 3 ASN A 94 ILE A 99 -1 O TYR A 97 N LEU A 57 SHEET 3 AA1 3 LEU A 86 CYS A 91 -1 N ALA A 89 O HIS A 96 SHEET 1 AA2 2 LEU B 86 CYS B 91 0 SHEET 2 AA2 2 ASN B 94 ILE B 99 -1 O HIS B 96 N ALA B 89 CRYST1 51.690 58.510 53.490 90.00 118.28 90.00 P 1 21 1 4 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 0.019346 0.000000 0.010408 0.00000 SCALE2 0.000000 0.017091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021229 0.00000