HEADER DNA BINDING PROTEIN 11-APR-18 5ZNX TITLE CRYSTAL STRUCTURE OF CM14-TREATED HLYU FROM VIBRIO VULNIFICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-98; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS CMCP6; SOURCE 3 ORGANISM_COMMON: VIBRIO VULNIFICUS STR. CMCP6; SOURCE 4 ORGANISM_TAXID: 216895; SOURCE 5 STRAIN: CMCP6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C43(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTC KEYWDS TRANSCRIPTION ACTIVATOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.PARK,S.KIM,I.JO,J.AHN,S.HONG,S.JEONG,Y.BAEK REVDAT 3 22-NOV-23 5ZNX 1 REMARK REVDAT 2 24-APR-19 5ZNX 1 JRNL REVDAT 1 10-APR-19 5ZNX 0 JRNL AUTH Z.W.LEE,B.S.KIM,K.K.JANG,Y.J.BANG,S.KIM,N.C.HA,Y.H.JUNG, JRNL AUTH 2 H.J.LEE,H.J.HAN,J.S.KIM,J.KIM,P.K.SAHU,L.S.JEONG,M.H.KIM, JRNL AUTH 3 S.H.CHOI JRNL TITL SMALL-MOLECULE INHIBITOR OF HLYU ATTENUATES VIRULENCE OF JRNL TITL 2 VIBRIO SPECIES. JRNL REF SCI REP V. 9 4346 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30867441 JRNL DOI 10.1038/S41598-019-39554-Y REMARK 2 REMARK 2 RESOLUTION. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 6758 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 REMARK 3 FREE R VALUE TEST SET COUNT : 309 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 2.6638 - 2.1140 0.89 2950 133 0.2433 0.3020 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) : 25.940 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 : 0.004 772 REMARK 3 ANGLE : 0.808 1037 REMARK 3 CHIRALITY : 0.039 123 REMARK 3 PLANARITY : 0.006 225 REMARK 3 DIHEDRAL : 2.485 585 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 5ZNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300007403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6980 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.114 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 19.70 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.20800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.600 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: 3JTH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH 8.0), 20% POLYETHYLENE REMARK 280 GLYCOL (PEG) 4K, 10% 2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 287K 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 90.19000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 17.57100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 17.57100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.09500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 17.57100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 17.57100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 135.28500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 17.57100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 17.57100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.09500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 17.57100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 17.57100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 135.28500 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 90.19000 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 LEU A 3 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 ALA A 72 -36.04 67.78 REMARK 500 GLN A 73 -20.31 -158.28 REMARK 500 LYS A 80 -62.95 -103.25 REMARK 500 GLU A 97 15.74 58.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 5ZNX A -3 98 PDB 5ZNX 5ZNX -3 98 SEQRES 1 A 102 GLY ALA MET GLY SER ASN LEU LYS ASP MET GLU GLN ASN SEQRES 2 A 102 SER ALA LYS ALA VAL VAL LEU LEU LYS ALA MET ALA ASN SEQRES 3 A 102 GLU ARG ARG LEU GLN ILE LEU CYS MET LEU HIS ASN GLN SEQRES 4 A 102 GLU LEU SER VAL GLY GLU LEU CYS ALA LYS LEU GLN LEU SEQRES 5 A 102 SER GLN SER ALA LEU SER GLN HIS LEU ALA TRP LEU ARG SEQRES 6 A 102 ARG ASP GLY LEU VAL THR THR ARG LYS GLU ALA GLN THR SEQRES 7 A 102 VAL TYR TYR THR LEU LYS SER GLU GLU VAL LYS ALA MET SEQRES 8 A 102 ILE LYS LEU LEU HIS SER LEU TYR CYS GLU GLU FORMUL 2 HOH *25(H2 O) HELIX 1 AA1 LYS A 4 ALA A 21 1 18 HELIX 2 AA2 ASN A 22 LEU A 32 1 11 HELIX 3 AA3 VAL A 39 GLN A 47 1 9 HELIX 4 AA4 SER A 49 ASP A 63 1 15 HELIX 5 AA5 SER A 81 CYS A 96 1 16 SHEET 1 AA1 3 LEU A 37 SER A 38 0 SHEET 2 AA1 3 THR A 74 LEU A 79 -1 O TYR A 77 N LEU A 37 SHEET 3 AA1 3 VAL A 66 GLU A 71 -1 N ARG A 69 O TYR A 76 CRYST1 35.142 35.142 180.380 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 0.028456 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005544 0.00000