HEADER DNA BINDING PROTEIN 30-OCT-19 6UUE TITLE THE SE-MET STRUCTURE OF THE VIBRIO VULNIFICUS TOXR PERIPLASMIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL ACTIVATOR TOXR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PERIPLASMIC DOMAIN; COMPND 5 SYNONYM: TRANSCRIPTIONAL REGULATOR,TRANSMEMBRANE TRANSCRIPTION COMPND 6 ACTIVATOR; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 672; SOURCE 4 GENE: TOXR, CRN46_04050, D8T65_08455, FORC36_0761; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SHUFFLE T7 EXPRESS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET16B; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETVVTOXRP KEYWDS TOXR, PERIPLASM, ALPHA-BETA, SENSOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.J.KULL,C.R.MIDGETT,R.A.SWINDELL REVDAT 1 17-JUN-20 6UUE 0 JRNL AUTH C.R.MIDGETT,R.A.SWINDELL,M.PELLEGRINI,F.JON KULL JRNL TITL A DISULFIDE CONSTRAINS THE TOXR PERIPLASMIC DOMAIN JRNL TITL 2 STRUCTURE, ALTERING ITS INTERACTIONS WITH TOXS AND JRNL TITL 3 BILE-SALTS. JRNL REF SCI REP V. 10 9002 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32488093 JRNL DOI 10.1038/S41598-020-66050-5 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 16585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1654 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 24.7800 - 3.1790 1.00 1353 155 0.1813 0.2195 REMARK 3 2 3.1790 - 2.5237 1.00 1296 140 0.2223 0.2166 REMARK 3 3 2.5237 - 2.2049 1.00 1268 143 0.2026 0.2585 REMARK 3 4 2.2049 - 2.0033 1.00 1258 141 0.2008 0.2199 REMARK 3 5 2.0033 - 1.8598 1.00 1278 130 0.1978 0.2437 REMARK 3 6 1.8598 - 1.7501 1.00 1241 139 0.2121 0.2180 REMARK 3 7 1.7501 - 1.6625 1.00 1237 138 0.2082 0.2184 REMARK 3 8 1.6625 - 1.5901 0.99 1230 139 0.1995 0.2518 REMARK 3 9 1.5901 - 1.5289 0.99 1232 135 0.2111 0.2448 REMARK 3 10 1.5289 - 1.4762 0.98 1213 137 0.2131 0.2533 REMARK 3 11 1.4762 - 1.4300 0.96 1193 127 0.2522 0.2835 REMARK 3 12 1.4300 - 1.3891 0.92 1133 130 0.2895 0.3091 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.72 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 6UUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000245202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.389 REMARK 200 RESOLUTION RANGE LOW (A) : 24.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.06322 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.18200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULFATE, 0.1 M HEPES PH REMARK 280 7.5, 0.1 M AMMONIUM FORMATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.98000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.78500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.78500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.98000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.26500 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 THR A 9 REMARK 465 ASN A 10 REMARK 465 PRO A 11 REMARK 465 SER A 12 REMARK 465 GLU A 13 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 ASN A 97 -145.76 -105.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 DBREF 6UUE A 9 104 UNP Q9RP86 Q9RP86_VIBVL 195 290 SEQADV 6UUE MSE A 1 UNP Q9RP86 INITIATING METHIONINE SEQADV 6UUE ALA A 2 UNP Q9RP86 EXPRESSION TAG SEQADV 6UUE HIS A 3 UNP Q9RP86 EXPRESSION TAG SEQADV 6UUE HIS A 4 UNP Q9RP86 EXPRESSION TAG SEQADV 6UUE HIS A 5 UNP Q9RP86 EXPRESSION TAG SEQADV 6UUE HIS A 6 UNP Q9RP86 EXPRESSION TAG SEQADV 6UUE HIS A 7 UNP Q9RP86 EXPRESSION TAG SEQADV 6UUE HIS A 8 UNP Q9RP86 EXPRESSION TAG SEQRES 1 A 104 MSE ALA HIS HIS HIS HIS HIS HIS THR ASN PRO SER GLU SEQRES 2 A 104 SER LYS PHE ARG LEU LEU GLU ASN VAL ASN GLY VAL GLU SEQRES 3 A 104 VAL LEU THR PRO LEU ASN HIS PRO PRO LEU GLN ALA TRP SEQRES 4 A 104 MSE PRO SER ILE ARG GLN CYS VAL ASN LYS TYR ALA GLU SEQRES 5 A 104 THR HIS THR GLY ASP SER ALA PRO VAL LYS VAL ILE ALA SEQRES 6 A 104 THR GLY GLY GLN GLY ASN GLN LEU ILE LEU ASN TYR ILE SEQRES 7 A 104 HIS THR LEU PRO HIS SER ASN GLU ASN VAL THR LEU ARG SEQRES 8 A 104 ILE PHE SER GLU GLN ASN ASP LEU GLY SER ILE CYS LYS MODRES 6UUE MSE A 40 MET MODIFIED RESIDUE HET MSE A 40 8 HET SO4 A 201 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *57(H2 O) HELIX 1 AA1 LEU A 36 ALA A 38 5 3 HELIX 2 AA2 TRP A 39 HIS A 54 1 16 HELIX 3 AA3 THR A 55 ALA A 59 5 5 HELIX 4 AA4 THR A 80 ASN A 87 5 8 HELIX 5 AA5 ASP A 98 CYS A 103 1 6 SHEET 1 AA1 5 PHE A 16 VAL A 22 0 SHEET 2 AA1 5 VAL A 25 PRO A 30 -1 O VAL A 27 N GLU A 20 SHEET 3 AA1 5 LYS A 62 GLY A 67 1 O ALA A 65 N LEU A 28 SHEET 4 AA1 5 GLN A 72 ILE A 78 -1 O ILE A 74 N THR A 66 SHEET 5 AA1 5 VAL A 88 PHE A 93 -1 O LEU A 90 N LEU A 75 SSBOND 1 CYS A 46 CYS A 103 1555 1555 2.05 LINK C TRP A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N PRO A 41 1555 1555 1.34 SITE 1 AC1 9 ARG A 17 LEU A 19 PRO A 35 LEU A 36 SITE 2 AC1 9 GLN A 37 GLN A 45 LYS A 49 HOH A 307 SITE 3 AC1 9 HOH A 311 CRYST1 39.960 40.530 49.570 90.00 90.00 90.00 P 21 21 21 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 0.025025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020173 0.00000