GenomeNet

Database: PDB
Entry: 6KCZ
LinkDB: 6KCZ
Original site: 6KCZ 
HEADER    HYDROLASE                               30-JUN-19   6KCZ              
TITLE     SOLUTION STRUCTURE OF THE ZNF-UBP DOMAIN OF USP20/VDU2                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 20;                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: DEUBIQUITINATING ENZYME 20,UBIQUITIN THIOESTERASE 20,       
COMPND   5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 20,VHL-INTERACTING            
COMPND   6 DEUBIQUITINATING ENZYME 2,HVDU2;                                     
COMPND   7 EC: 3.4.19.12;                                                       
COMPND   8 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: USP20, KIAA1003, LSFR3A, VDU2;                                 
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    HYDROLASE                                                             
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    Y.YANG,Y.WEN,N.ZHANG                                                  
REVDAT   3   04-SEP-19 6KCZ    1       JRNL                                     
REVDAT   2   21-AUG-19 6KCZ    1       SPRSDE JRNL                              
REVDAT   1   17-JUL-19 6KCZ    0                                                
SPRSDE     21-AUG-19 6KCZ      5Z4I                                             
JRNL        AUTH   Y.YANG,Y.DING,C.ZHOU,Y.WEN,N.ZHANG                           
JRNL        TITL   STRUCTURAL AND FUNCTIONAL STUDIES OF USP20 ZNF-UBP DOMAIN BY 
JRNL        TITL 2 NMR.                                                         
JRNL        REF    PROTEIN SCI.                  V.  28  1606 2019              
JRNL        REFN                   ESSN 1469-896X                               
JRNL        PMID   31278784                                                     
JRNL        DOI    10.1002/PRO.3675                                             
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER A. T. ET.AL.                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6KCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-19.                  
REMARK 100 THE DEPOSITION ID IS D_1300012723.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 150                                
REMARK 210  PRESSURE                       : 1 PA                               
REMARK 210  SAMPLE CONTENTS                : 0.6 MM [U-99% 13C; U-99% 15N]      
REMARK 210                                   USP20, 90% H2O/10% D2O; 0.6 MM     
REMARK 210                                   [U-99% 15N] USP20, 90% H2O/10%     
REMARK 210                                   D2O; 0.6 MM [U-99% 13C] USP20,     
REMARK 210                                   100% D2O                           
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 3D HNCA; 3D        
REMARK 210                                   HN(CO)CA; 3D HNCO; 3D HN(CA)CO;    
REMARK 210                                   3D HNCACB; 3D CBCA(CO)NH; 3D 1H-   
REMARK 210                                   15N NOESY; 2D 1H-13C HSQC; 3D 1H-  
REMARK 210                                   13C NOESY ALIPHATIC; 3D HCCH-      
REMARK 210                                   TOCSY; 3D H(CCO)NH; 3D C(CO)NH     
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : X-PLOR NIH, CARA                   
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 60                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
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                                             
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   O    LEU A    24     H    LYS A    27              1.49            
REMARK 500   H    ASN A    39     OG1  THR A    77              1.55            
REMARK 500   N    ASN A    39     OG1  THR A    77              2.12            
REMARK 500   O    GLY A    54     N    SER A    56              2.15            
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  1 SER A   4      168.16     55.41                                   
REMARK 500  1 SER A  26       11.21    -68.33                                   
REMARK 500  1 THR A  36     -177.01    166.30                                   
REMARK 500  1 VAL A  46      -20.09    -39.57                                   
REMARK 500  1 ALA A  47       54.45   -149.29                                   
REMARK 500  1 GLU A  55      -37.46    -25.62                                   
REMARK 500  1 SER A  56      -43.47    -28.33                                   
REMARK 500  1 PHE A  57      -92.08   -118.44                                   
REMARK 500  1 LYS A  69       16.54     56.01                                   
REMARK 500  1 LEU A  76        9.01    -68.29                                   
REMARK 500  1 PHE A  79       56.53     79.48                                   
REMARK 500  1 TYR A  84        2.61    -68.77                                   
REMARK 500  1 ALA A  85      -71.35    -99.87                                   
REMARK 500  1 GLU A  93        2.04    -46.73                                   
REMARK 500  1 GLN A  94      -19.89     61.36                                   
REMARK 500  1 ALA A  97      146.38   -171.58                                   
REMARK 500  2 SER A   4     -172.80    168.24                                   
REMARK 500  2 THR A  36     -176.94    166.64                                   
REMARK 500  2 VAL A  46      -20.95    -39.45                                   
REMARK 500  2 ALA A  47       52.96   -150.13                                   
REMARK 500  2 GLU A  55      -37.34    -25.78                                   
REMARK 500  2 SER A  56      -43.39    -28.47                                   
REMARK 500  2 PHE A  57      -92.28   -118.24                                   
REMARK 500  2 LYS A  69       16.71     56.87                                   
REMARK 500  2 LEU A  76        7.02    -67.87                                   
REMARK 500  2 PHE A  79       54.62     78.99                                   
REMARK 500  2 TYR A  84        2.49    -69.86                                   
REMARK 500  2 ALA A  85      -70.77   -100.67                                   
REMARK 500  2 GLU A  93        2.44    -49.79                                   
REMARK 500  2 GLN A  94      -20.08     63.86                                   
REMARK 500  2 ALA A  97       87.32   -154.47                                   
REMARK 500  2 ALA A  98       71.71   -163.26                                   
REMARK 500  3 ASP A   3      102.65     54.90                                   
REMARK 500  3 SER A   4     -176.82    168.30                                   
REMARK 500  3 SER A  26       11.64    -69.58                                   
REMARK 500  3 THR A  36     -176.58    165.13                                   
REMARK 500  3 TRP A  41       93.56   -161.75                                   
REMARK 500  3 VAL A  46      -20.54    -39.63                                   
REMARK 500  3 ALA A  47       47.31   -147.66                                   
REMARK 500  3 GLU A  55      -37.21    -24.51                                   
REMARK 500  3 SER A  56      -42.80    -29.03                                   
REMARK 500  3 PHE A  57      -92.91   -117.79                                   
REMARK 500  3 LYS A  69       16.50     47.75                                   
REMARK 500  3 PHE A  79       49.87     79.59                                   
REMARK 500  3 TYR A  84        2.54    -68.09                                   
REMARK 500  3 ALA A  85      -70.26   -100.60                                   
REMARK 500  3 GLU A  93        2.33    -49.57                                   
REMARK 500  3 GLN A  94      -19.74     61.00                                   
REMARK 500  3 ALA A  98       59.22   -156.77                                   
REMARK 500  4 ASP A   3     -124.31    -84.85                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     361 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 101  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A   8   SG                                                     
REMARK 620 2 HIS A  10   ND1 114.0                                              
REMARK 620 3 CYS A  83   SG  108.7 103.4                                        
REMARK 620 4 CYS A  86   SG  113.6 102.3 114.4                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 102  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A  30   SG                                                     
REMARK 620 2 CYS A  33   SG  107.9                                              
REMARK 620 3 CYS A  53   SG  116.3 107.4                                        
REMARK 620 4 HIS A  60   ND1 115.0 102.2 107.0                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 103  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A  43   SG                                                     
REMARK 620 2 CYS A  48   SG  107.5                                              
REMARK 620 3 HIS A  64   NE2 107.7 109.9                                        
REMARK 620 4 HIS A  70   ND1 111.9 106.3 113.3                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 103                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 26901   RELATED DB: BMRB                                 
DBREF  6KCZ A    1    99  UNP    Q9Y2K6   UBP20_HUMAN      1     99             
SEQRES   1 A   99  MET GLY ASP SER ARG ASP LEU CYS PRO HIS LEU ASP SER          
SEQRES   2 A   99  ILE GLY GLU VAL THR LYS GLU ASP LEU LEU LEU LYS SER          
SEQRES   3 A   99  LYS GLY THR CYS GLN SER CYS GLY VAL THR GLY PRO ASN          
SEQRES   4 A   99  LEU TRP ALA CYS LEU GLN VAL ALA CYS PRO TYR VAL GLY          
SEQRES   5 A   99  CYS GLY GLU SER PHE ALA ASP HIS SER THR ILE HIS ALA          
SEQRES   6 A   99  GLN ALA LYS LYS HIS ASN LEU THR VAL ASN LEU THR THR          
SEQRES   7 A   99  PHE ARG LEU TRP CYS TYR ALA CYS GLU LYS GLU VAL PHE          
SEQRES   8 A   99  LEU GLU GLN ARG LEU ALA ALA PRO                              
HET     ZN  A 101       1                                                       
HET     ZN  A 102       1                                                       
HET     ZN  A 103       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    3(ZN 2+)                                                     
HELIX    1 AA1 THR A   18  SER A   26  1                                   9    
HELIX    2 AA2 ASP A   59  LYS A   68  1                                  10    
SHEET    1 AA1 5 VAL A  51  GLY A  52  0                                        
SHEET    2 AA1 5 TRP A  41  CYS A  43 -1  N  TRP A  41   O  GLY A  52           
SHEET    3 AA1 5 LEU A  72  VAL A  74 -1  O  VAL A  74   N  ALA A  42           
SHEET    4 AA1 5 LEU A  81  CYS A  83 -1  O  TRP A  82   N  THR A  73           
SHEET    5 AA1 5 LYS A  88  VAL A  90 -1  O  VAL A  90   N  LEU A  81           
LINK         SG  CYS A   8                ZN    ZN A 101     1555   1555  2.32  
LINK         ND1 HIS A  10                ZN    ZN A 101     1555   1555  2.02  
LINK         SG  CYS A  30                ZN    ZN A 102     1555   1555  2.32  
LINK         SG  CYS A  33                ZN    ZN A 102     1555   1555  2.30  
LINK         SG  CYS A  43                ZN    ZN A 103     1555   1555  2.29  
LINK         SG  CYS A  48                ZN    ZN A 103     1555   1555  2.29  
LINK         SG  CYS A  53                ZN    ZN A 102     1555   1555  2.30  
LINK         ND1 HIS A  60                ZN    ZN A 102     1555   1555  2.01  
LINK         NE2 HIS A  64                ZN    ZN A 103     1555   1555  1.99  
LINK         ND1 HIS A  70                ZN    ZN A 103     1555   1555  1.99  
LINK         SG  CYS A  83                ZN    ZN A 101     1555   1555  2.29  
LINK         SG  CYS A  86                ZN    ZN A 101     1555   1555  2.32  
SITE     1 AC1  5 CYS A   8  PRO A   9  HIS A  10  CYS A  83                    
SITE     2 AC1  5 CYS A  86                                                     
SITE     1 AC2  4 CYS A  30  CYS A  33  CYS A  53  HIS A  60                    
SITE     1 AC3  4 CYS A  43  CYS A  48  HIS A  64  HIS A  70                    
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
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      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000                         
MODEL        1                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
DBGET integrated database retrieval system