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Database: PDB
Entry: 5E3D
LinkDB: 5E3D
Original site: 5E3D 
HEADER    DNA BINDING PROTEIN                     02-OCT-15   5E3D              
TITLE     CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH SEED7
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PEREGRIN;                                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 626-740;                                      
COMPND   5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1,PROTEIN     
COMPND   6 BR140;                                                               
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: BRPF1, BR140;                                                  
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1(BRPF1), MONOCYTIC     
KEYWDS   2 LEUKEMIA ZINC-FINGER (MOZ), INHIBITOR, TRANSCRIPTION, DNA BINDING    
KEYWDS   3 PROTEIN                                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.ZHU,A.CAFLISCH                                                      
REVDAT   2   22-JUN-16 5E3D    1       JRNL                                     
REVDAT   1   25-MAY-16 5E3D    0                                                
JRNL        AUTH   J.ZHU,A.CAFLISCH                                             
JRNL        TITL   TWENTY CRYSTAL STRUCTURES OF BROMODOMAIN AND PHD FINGER      
JRNL        TITL 2 CONTAINING PROTEIN 1 (BRPF1)/LIGAND COMPLEXES REVEAL         
JRNL        TITL 3 CONSERVED BINDING MOTIFS AND RARE INTERACTIONS.              
JRNL        REF    J.MED.CHEM.                   V.  59  5555 2016              
JRNL        REFN                   ISSN 0022-2623                               
JRNL        PMID   27167503                                                     
JRNL        DOI    10.1021/ACS.JMEDCHEM.6B00215                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.71 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (1.10_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 : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 40.22                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.360                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 14776                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.194                           
REMARK   3   R VALUE            (WORKING SET) : 0.193                           
REMARK   3   FREE R VALUE                     : 0.222                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.010                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 740                             
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 40.2340 -  2.9210    0.99     2912   154  0.1746 0.1853        
REMARK   3     2  2.9210 -  2.3185    1.00     2829   149  0.2247 0.2969        
REMARK   3     3  2.3185 -  2.0254    1.00     2770   146  0.1966 0.2366        
REMARK   3     4  2.0254 -  1.8403    1.00     2780   147  0.2182 0.2613        
REMARK   3     5  1.8403 -  1.7100    0.99     2745   144  0.2410 0.3194        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
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)     : 0.180            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.160           
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      :  0.007            977                                  
REMARK   3   ANGLE     :  0.710           1322                                  
REMARK   3   CHIRALITY :  0.043            141                                  
REMARK   3   PLANARITY :  0.005            174                                  
REMARK   3   DIHEDRAL  : 14.934            598                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : 1                                          
REMARK   3   TLS GROUP : 1                                                      
REMARK   3    SELECTION: ALL                                                    
REMARK   3    ORIGIN FOR THE GROUP (A):  14.8064 -22.5434   0.5016              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:   0.3209 T22:   0.3044                                     
REMARK   3      T33:   0.3046 T12:  -0.1339                                     
REMARK   3      T13:  -0.0532 T23:   0.0460                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:   3.2971 L22:   6.3754                                     
REMARK   3      L33:   2.4937 L12:  -1.0939                                     
REMARK   3      L13:   0.8432 L23:  -1.6162                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:   0.0624 S12:  -0.4228 S13:  -0.2708                       
REMARK   3      S21:   0.6974 S22:  -0.2497 S23:  -0.1323                       
REMARK   3      S31:  -0.1560 S32:   0.0309 S33:   0.1570                       
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 5E3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-15.                  
REMARK 100 THE DEPOSITION ID IS D_1000214281.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 05-JUL-15                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 5.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X06SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.99987                            
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : PSI PILATUS 6M                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 14799                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.710                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.220                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.7                               
REMARK 200  DATA REDUNDANCY                : 9.500                              
REMARK 200  R MERGE                    (I) : 0.03100                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 30.3000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.80                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.1                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 9.60                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.40500                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.100                              
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: 4LC2                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 49.27                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH5.5, 0.15 M      
REMARK 280  SODIUM NITRATE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP,         
REMARK 280  TEMPERATURE 277K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z+2/3                                            
REMARK 290       3555   -X+Y,-X,Z+1/3                                           
REMARK 290       4555   Y,X,-Z                                                  
REMARK 290       5555   X-Y,-Y,-Z+1/3                                           
REMARK 290       6555   -X,-X+Y,-Z+2/3                                          
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 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       41.62000            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       20.81000            
REMARK 290   SMTRY1   4 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   5  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       20.81000            
REMARK 290   SMTRY1   6 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       41.62000            
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: 140 ANGSTROM**2                           
REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375      HOH A 948  LIES ON A SPECIAL POSITION.                          
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     SER A   625                                                      
REMARK 465     MET A   626                                                      
REMARK 465     GLU A   627                                                      
REMARK 465     GLY A   740                                                      
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     LYS A 670    CD   CE   NZ                                        
REMARK 470     LYS A 706    NZ                                                  
REMARK 470     GLN A 731    CD   OE1  NE2                                       
REMARK 470     LYS A 738    CE   NZ                                             
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 5JL A 801                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 802                 
DBREF  5E3D A  626   740  UNP    P55201   BRPF1_HUMAN    626    740             
SEQADV 5E3D SER A  625  UNP  P55201              EXPRESSION TAG                 
SEQRES   1 A  116  SER MET GLU MET GLN LEU THR PRO PHE LEU ILE LEU LEU          
SEQRES   2 A  116  ARG LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY          
SEQRES   3 A  116  ASN ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO          
SEQRES   4 A  116  ASP TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE          
SEQRES   5 A  116  THR MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN          
SEQRES   6 A  116  PHE ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER          
SEQRES   7 A  116  ASN CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR          
SEQRES   8 A  116  ARG ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL          
SEQRES   9 A  116  LEU ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY              
HET    5JL  A 801      12                                                       
HET    NO3  A 802       4                                                       
HETNAM     5JL 2,8-DITHIOXO-1,2,3,7,8,9-HEXAHYDRO-6H-PURIN-6-ONE                
HETNAM     NO3 NITRATE ION                                                      
FORMUL   2  5JL    C5 H4 N4 O S2                                                
FORMUL   3  NO3    N O3 1-                                                      
FORMUL   4  HOH   *75(H2 O)                                                     
HELIX    1 AA1 GLN A  629  ASP A  648  1                                  20    
HELIX    2 AA2 ASP A  664  HIS A  668  5                                   5    
HELIX    3 AA3 ASP A  674  ALA A  684  1                                  11    
HELIX    4 AA4 ASN A  689  ASN A  708  1                                  20    
HELIX    5 AA5 THR A  712  MET A  739  1                                  28    
SITE     1 AC1  6 ILE A 652  VAL A 657  VAL A 662  ASN A 708                    
SITE     2 AC1  6 PHE A 714  HOH A 907                                          
SITE     1 AC2  7 SER A 702  LEU A 705  LYS A 706  TYR A 715                    
SITE     2 AC2  7 VAL A 719  ARG A 722  HOH A 910                               
CRYST1   60.730   60.730   62.430  90.00  90.00 120.00 P 32 2 1      6          
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      0.016466  0.009507  0.000000        0.00000                         
SCALE2      0.000000  0.019014  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.016018        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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