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