HEADER    TRANSCRIPTION                           18-MAR-18   6G0D              
TITLE     BRD4 (BD1) IN COMPLEX WITH APSC-DERIVED LIGANDS (E.G. LY294002)       
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;                          
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: BD1;                                                       
COMPND   5 SYNONYM: PROTEIN HUNK1;                                              
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: BRD4, HUNK1;                                                   
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4                               
KEYWDS    BRD4, TRANSCRIPTION                                                   
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.PRETZEL,L.HUMBECK                                                   
REVDAT   2   17-JAN-24 6G0D    1       JRNL                                     
REVDAT   1   08-JAN-20 6G0D    0                                                
JRNL        AUTH   L.HUMBECK,J.PRETZEL,S.SPITZER,O.KOCH                         
JRNL        TITL   DISCOVERY OF AN UNEXPECTED SIMILARITY IN LIGAND BINDING      
JRNL        TITL 2 BETWEEN BRD4 AND PPARGAMMA                                   
JRNL        REF    CHEMRXIV                                   2019              
JRNL        REFN                   ISSN 2573-2293                               
JRNL        DOI    10.26434/CHEMRXIV.11472618                                   
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.31 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.10.1-2155                                   
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) : 1.31                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 39.79                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.330                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.2                           
REMARK   3   NUMBER OF REFLECTIONS             : 31670                          
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) : 0.202                           
REMARK   3   FREE R VALUE                     : 0.236                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.090                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1611                            
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 39.8092 -  3.0089    1.00     2702   146  0.1661 0.1908        
REMARK   3     2  3.0089 -  2.3883    1.00     2569   132  0.1999 0.2422        
REMARK   3     3  2.3883 -  2.0864    0.99     2546   113  0.2031 0.2175        
REMARK   3     4  2.0864 -  1.8957    0.97     2462   124  0.2184 0.2739        
REMARK   3     5  1.8957 -  1.7598    1.00     2498   145  0.2021 0.2260        
REMARK   3     6  1.7598 -  1.6560    1.00     2491   138  0.1882 0.2656        
REMARK   3     7  1.6560 -  1.5731    1.00     2510   141  0.1897 0.2194        
REMARK   3     8  1.5731 -  1.5046    1.00     2480   134  0.2146 0.2476        
REMARK   3     9  1.5046 -  1.4467    0.97     2423   130  0.3001 0.3543        
REMARK   3    10  1.4467 -  1.3968    1.00     2466   142  0.2659 0.2919        
REMARK   3    11  1.3968 -  1.3531    1.00     2494   137  0.2691 0.2958        
REMARK   3    12  1.3531 -  1.3144    0.98     2418   129  0.2757 0.3047        
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)     : 0.140            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.330           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 20.16                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 15.97                          
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      :  0.006           1147                                  
REMARK   3   ANGLE     :  0.793           1562                                  
REMARK   3   CHIRALITY :  0.071            162                                  
REMARK   3   PLANARITY :  0.005            202                                  
REMARK   3   DIHEDRAL  : 20.479            447                                  
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 6G0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAR-18.                  
REMARK 100 THE DEPOSITION ID IS D_1200008897.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 25-AUG-16                          
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               : SLS                                
REMARK 200  BEAMLINE                       : X10SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.999850                           
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M-F               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS 1.11.2016                      
REMARK 200  DATA SCALING SOFTWARE          : AIMLESS CCP4 PACKAGE 7.0           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 31937                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.314                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 39.791                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.9                               
REMARK 200  DATA REDUNDANCY                : 8.910                              
REMARK 200  R MERGE                    (I) : 0.07600                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 20.0500                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.35                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.9                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.93500                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.700                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER 1.10.1-2155                                    
REMARK 200 STARTING MODEL: 3MXF                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 42.80                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FLUORIDE, 20 % (W/V) PEG    
REMARK 280  3350, CRYO PROTECTION: 20% ETHYLENE GLYCOL, PH 7.5, VAPOR           
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 277K                           
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       19.14750            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       39.79100            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       21.43400            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       39.79100            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       19.14750            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       21.43400            
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 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2                           
REMARK 350 SURFACE AREA OF THE COMPLEX: 7650 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 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    LEU A  94       71.60   -119.28                                   
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 EDO A 201                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue LY2 A 202                 
DBREF  6G0D A   42   168  UNP    O60885   BRD4_HUMAN      42    168             
SEQADV 6G0D MET A   43  UNP  O60885    THR    43 ENGINEERED MUTATION            
SEQRES   1 A  127  SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN          
SEQRES   2 A  127  LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU          
SEQRES   3 A  127  ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA          
SEQRES   4 A  127  TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN          
SEQRES   5 A  127  LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP          
SEQRES   6 A  127  MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR          
SEQRES   7 A  127  TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET          
SEQRES   8 A  127  PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP          
SEQRES   9 A  127  ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU          
SEQRES  10 A  127  GLN LYS ILE ASN GLU LEU PRO THR GLU GLU                      
HET    EDO  A 201       4                                                       
HET    LY2  A 202      40                                                       
HETNAM     EDO 1,2-ETHANEDIOL                                                   
HETNAM     LY2 2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE                       
HETSYN     EDO ETHYLENE GLYCOL                                                  
HETSYN     LY2 2-(4-MORPHOLINYL)-8-PHENYL-4H-1-BENZOPYRAN-4-ONE                 
FORMUL   2  EDO    C2 H6 O2                                                     
FORMUL   3  LY2    C19 H17 N O3                                                 
FORMUL   4  HOH   *145(H2 O)                                                    
HELIX    1 AA1 THR A   60  VAL A   69  1                                  10    
HELIX    2 AA2 VAL A   69  LYS A   76  1                                   8    
HELIX    3 AA3 ALA A   80  GLN A   84  5                                   5    
HELIX    4 AA4 ASP A   96  ILE A  101  1                                   6    
HELIX    5 AA5 ASP A  106  ASN A  116  1                                  11    
HELIX    6 AA6 ASN A  121  ASN A  140  1                                  20    
HELIX    7 AA7 ASP A  144  ASN A  162  1                                  19    
SITE     1 AC1  6 ILE A 100  ILE A 101  LYS A 102  THR A 103                    
SITE     2 AC1  6 ASN A 135  HOH A 337                                          
SITE     1 AC2  8 TRP A  81  PRO A  82  PHE A  83  VAL A  87                    
SITE     2 AC2  8 LEU A  92  LEU A  94  ASN A 140  HOH A 317                    
CRYST1   38.295   42.868   79.582  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      0.026113  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.023327  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.012566        0.00000