HEADER    STRUCTURAL PROTEIN                      19-MAR-20   7BOL              
TITLE     UBIQUITIN-CONJUGATING ENZYME, UBE2D2                                  
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2;                        
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: UBIQUITIN-CONJUGATING ENZYME UBE2D2;                        
COMPND   5 EC: 2.3.2.23,2.3.2.24;                                               
COMPND   6 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: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B;                     
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    UBIQUITIN-CONJUGATING ENZYME, UBE2D2, STRUCTURAL PROTEIN              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.O.LEE,K.S.RYU,S.-W.CHI                                              
REVDAT   3   29-NOV-23 7BOL    1       REMARK                                   
REVDAT   2   20-APR-22 7BOL    1       JRNL                                     
REVDAT   1   24-MAR-21 7BOL    0                                                
JRNL        AUTH   M.S.LEE,S.O.LEE,J.CHOI,M.RYU,M.K.LEE,J.H.KIM,E.HWANG,        
JRNL        AUTH 2 C.K.LEE,S.W.CHI,K.S.RYU                                      
JRNL        TITL   MUL1-RING RECRUITS THE SUBSTRATE, P53-TAD AS A COMPLEX WITH  
JRNL        TITL 2 UBE2D2-UB CONJUGATE.                                         
JRNL        REF    FEBS J.                                    2022              
JRNL        REFN                   ISSN 1742-464X                               
JRNL        PMID   35048531                                                     
JRNL        DOI    10.1111/FEBS.16360                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 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) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 26.48                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.500                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 96.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 14967                          
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                     : 0.219                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.820                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 721                             
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 26.4760 -  3.0716    1.00     3074   147  0.1763 0.1871        
REMARK   3     2  3.0716 -  2.4385    0.99     2893   143  0.1937 0.2135        
REMARK   3     3  2.4385 -  2.1304    0.98     2883   137  0.1819 0.2100        
REMARK   3     4  2.1304 -  1.9357    0.97     2783   157  0.2056 0.2776        
REMARK   3     5  1.9357 -  1.7970    0.91     2613   137  0.2609 0.3002        
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)     : 0.230            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 15.47                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 18.39                          
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           1220                                  
REMARK   3   ANGLE     :  0.919           1664                                  
REMARK   3   CHIRALITY :  0.054            179                                  
REMARK   3   PLANARITY :  0.006            217                                  
REMARK   3   DIHEDRAL  : 19.073            743                                  
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 7BOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-20.                  
REMARK 100 THE DEPOSITION ID IS D_1300016217.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 04-MAY-16                          
REMARK 200  TEMPERATURE           (KELVIN) : 93                                 
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : PAL/PLS                            
REMARK 200  BEAMLINE                       : 7A (6B, 6C1)                       
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9793                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 270                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 14967                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.797                              
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     (%) : 96.8                               
REMARK 200  DATA REDUNDANCY                : 6.100                              
REMARK 200  R MERGE                    (I) : 0.07200                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 26.3000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: MAD                                            
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: 2ESK                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 48.12                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE 0.1 M SODIUM      
REMARK 280  CITRATE PH 5.6 1.0 M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING      
REMARK 280  DROP, TEMPERATURE 291K                                              
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       24.18700            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       31.63500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       26.09250            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       31.63500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       24.18700            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       26.09250            
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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500  HD22  ASN A   114     O    HOH A   201              1.32            
REMARK 500   ND2  ASN A   114     O    HOH A   201              1.97            
REMARK 500   O    HOH A   302     O    HOH A   303              2.05            
REMARK 500   O    HOH A   206     O    HOH A   248              2.11            
REMARK 500   O    HOH A   299     O    HOH A   322              2.13            
REMARK 500   OH   TYR A   134     O    HOH A   202              2.15            
REMARK 500   O    HOH A   202     O    HOH A   278              2.17            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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  19       94.74    -66.01                                   
REMARK 500    ASP A  42      -13.58     76.48                                   
REMARK 500    ARG A  90     -103.06   -131.81                                   
REMARK 500    ASP A 130       77.93   -152.92                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  7BOL A    1   147  UNP    P62837   UB2D2_HUMAN      1    147             
SEQADV 7BOL SER A    0  UNP  P62837              EXPRESSION TAG                 
SEQRES   1 A  148  SER MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP          
SEQRES   2 A  148  LEU ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO          
SEQRES   3 A  148  VAL GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET          
SEQRES   4 A  148  GLY PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE          
SEQRES   5 A  148  LEU THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO          
SEQRES   6 A  148  PRO LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN          
SEQRES   7 A  148  ILE ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG          
SEQRES   8 A  148  SER GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU          
SEQRES   9 A  148  LEU SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP          
SEQRES  10 A  148  ASP PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR          
SEQRES  11 A  148  ASP ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR          
SEQRES  12 A  148  GLN LYS TYR ALA MET                                          
FORMUL   2  HOH   *124(H2 O)                                                    
HELIX    1 AA1 SER A    0  ASP A   16  1                                  17    
HELIX    2 AA2 LEU A   86  ARG A   90  5                                   5    
HELIX    3 AA3 THR A   98  ASP A  112  1                                  15    
HELIX    4 AA4 VAL A  120  ASP A  130  1                                  11    
HELIX    5 AA5 ASP A  130  ALA A  146  1                                  17    
SHEET    1 AA1 4 CYS A  21  PRO A  25  0                                        
SHEET    2 AA1 4 HIS A  32  MET A  38 -1  O  GLN A  34   N  GLY A  24           
SHEET    3 AA1 4 VAL A  49  HIS A  55 -1  O  PHE A  50   N  ILE A  37           
SHEET    4 AA1 4 LYS A  66  PHE A  69 -1  O  LYS A  66   N  HIS A  55           
CISPEP   1 TYR A   60    PRO A   61          0         5.85                     
CRYST1   48.374   52.185   63.270  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      0.020672  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.019163  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.015805        0.00000