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Database: PDB
Entry: 2JV0
LinkDB: 2JV0
Original site: 2JV0 
HEADER    TRANSCRIPTION                           10-SEP-07   2JV0              
TITLE     SET DOMAIN OF RIZ1 TUMOR SUPPRESSOR (PRDM2)                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PR DOMAIN ZINC FINGER PROTEIN 2;                           
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: SET DOMAIN RESIDUES 1-161;                                 
COMPND   5 SYNONYM: PR DOMAIN-CONTAINING PROTEIN 2, RETINOBLASTOMA PROTEIN-     
COMPND   6 INTERACTING ZINC FINGER PROTEIN, ZINC FINGER PROTEIN RIZ, MTE-BINDING
COMPND   7 PROTEIN, MTB-ZF, GATA-3-BINDING PROTEIN G3B;                         
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 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: PRDM2, RIZ;                                                    
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PKG-PBR                                    
KEYWDS    SET DOMAIN, PR DOMAIN, RIZ1, PRDM2, PROTEIN LYSINE METHYLTRANSFERASE, 
KEYWDS   2 HISTONE LYSINE METHYLTRANSFERASE, HKMT, ACTIVATOR, ALTERNATIVE       
KEYWDS   3 INITIATION, DNA-BINDING, METAL-BINDING, NUCLEUS, PHOSPHORYLATION,    
KEYWDS   4 TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC-FINGER                 
EXPDTA    SOLUTION NMR                                                          
NUMMDL    16                                                                    
AUTHOR    K.BRIKNAROVA                                                          
REVDAT   5   27-JUL-11 2JV0    1       HETNAM HETSYN REMARK                     
REVDAT   4   13-JUL-11 2JV0    1       VERSN                                    
REVDAT   3   29-DEC-09 2JV0    1       HET                                      
REVDAT   2   24-FEB-09 2JV0    1       VERSN                                    
REVDAT   1   22-JAN-08 2JV0    0                                                
JRNL        AUTH   K.BRIKNAROVA,X.ZHOU,A.SATTERTHWAIT,D.W.HOYT,K.R.ELY,S.HUANG  
JRNL        TITL   STRUCTURAL STUDIES OF THE SET DOMAIN FROM RIZ1 TUMOR         
JRNL        TITL 2 SUPPRESSOR                                                   
JRNL        REF    BIOCHEM.BIOPHYS.RES.COMMUN.   V. 366   807 2008              
JRNL        REFN                   ISSN 0006-291X                               
JRNL        PMID   18082620                                                     
JRNL        DOI    10.1016/J.BBRC.2007.12.034                                   
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR_NIH 2.13                                      
REMARK   3   AUTHORS     : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE             
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2JV0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-07.                  
REMARK 100 THE RCSB ID CODE IS RCSB100324.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.8                                
REMARK 210  IONIC STRENGTH                 : 0.082                              
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.4-1 MM [U-99% 15N] ENTITY_1,     
REMARK 210                                   20 MM POTASSIUM PHOSPHATE, 50 MM   
REMARK 210                                   POTASSIUM CHLORIDE, 2.5 MM DTT,    
REMARK 210                                   0-2 MM EDTA, 0-4.5 MM S-ADENOSYL-  
REMARK 210                                   L-HOMOCYSTEINE, 90% H2O/10% D2O;   
REMARK 210                                   0.8 MM [U-99% 13C; U-99% 15N]      
REMARK 210                                   ENTITY_1, 20 MM POTASSIUM          
REMARK 210                                   PHOSPHATE, 50 MM POTASSIUM         
REMARK 210                                   CHLORIDE, 2.5 MM DTT, 0-2 MM       
REMARK 210                                   EDTA, 0-4.5 MM S-ADENOSYL-L-       
REMARK 210                                   HOMOCYSTEINE, 90% H2O/10% D2O;     
REMARK 210                                   0.5-1 MM [U-99% 13C; U-99% 15N;    
REMARK 210                                   80% 2H] ENTITY_1, 20 MM POTASSIUM  
REMARK 210                                   PHOSPHATE, 50 MM POTASSIUM         
REMARK 210                                   CHLORIDE, 2.5 MM DTT, 1-2 MM       
REMARK 210                                   EDTA, 0-4.5 MM S-ADENOSYL-L-       
REMARK 210                                   HOMOCYSTEINE, 90% H2O/10% D2O;     
REMARK 210                                   0.9 MM [U-99% 15N; 80% 2H]         
REMARK 210                                   ENTITY_1, 20 MM POTASSIUM          
REMARK 210                                   PHOSPHATE, 50 MM POTASSIUM         
REMARK 210                                   CHLORIDE, 2.5 MM DTT, 1-2 MM       
REMARK 210                                   EDTA, 4.5 MM S-ADENOSYL-L-         
REMARK 210                                   HOMOCYSTEINE, 90% H2O/10% D2O      
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D 1H-15N NOESY; 3D 1H-13C         
REMARK 210                                   NOESY; 3D 1H-13C AROMATIC NOESY;   
REMARK 210                                   4D 15N,15N NOESY; 3D CBCA(CO)NH;   
REMARK 210                                   3D C(CO)NH; 3D HNCACB; 3D H(CCO)   
REMARK 210                                   NH; 3D HCCH-TOCSY                  
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ; 750 MHZ                   
REMARK 210  SPECTROMETER MODEL             : AVANCE; INOVA                      
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER; VARIAN                     
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : FELIX, ARIA 1.2                    
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS             
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 40                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 16                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST 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   OD1  ASN A   112     H    LEU A   137              1.26            
REMARK 500   H    GLY A    53     O    THR A   126              1.30            
REMARK 500   O    PRO A    34     H    ALA A    36              1.37            
REMARK 500   OD1  ASN A    72     H    VAL A    73              1.44            
REMARK 500   O    VAL A    73     H    MET A    75              1.47            
REMARK 500   H    TYR A    80     O    GLY A    84              1.47            
REMARK 500   OD1  ASN A   145     H    ILE A   148              1.49            
REMARK 500   H    SER A    35     O    ARG A    41              1.52            
REMARK 500   O    PHE A    33     H    GLY A    43              1.53            
REMARK 500   HG1  THR A    91    HH11  ARG A   100              1.55            
REMARK 500   H    THR A    47     H    LYS A    48              1.55            
REMARK 500   H    ASP A     2     H    GLN A     3              1.56            
REMARK 500   H    PHE A    33     O    GLY A    43              1.57            
REMARK 500  HG21  VAL A    60     H    GLY A    61              1.57            
REMARK 500   O    GLU A   153     H    ALA A   157              1.57            
REMARK 500  HG23  VAL A    60     H    ASN A    97              1.58            
REMARK 500   HA   PRO A    34     HA   ILE A    42              1.59            
REMARK 500   H    VAL A    78     O    MET A    86              1.59            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500  8 TYR A 124   CB  -  CG  -  CD2 ANGL. DEV. =  -3.8 DEGREES          
REMARK 500 12 TYR A 124   CB  -  CG  -  CD2 ANGL. DEV. =  -4.0 DEGREES          
REMARK 500 13 TYR A  80   CB  -  CG  -  CD2 ANGL. DEV. =  -3.9 DEGREES          
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   0      -46.42     75.39                                   
REMARK 500  1 ASP A   2       -6.48   -150.08                                   
REMARK 500  1 GLN A   3      179.74    -52.80                                   
REMARK 500  1 ALA A  10      106.46     67.73                                   
REMARK 500  1 ALA A  11      -76.54   -129.86                                   
REMARK 500  1 THR A  12      -46.92    151.52                                   
REMARK 500  1 PRO A  27     -112.08    -36.25                                   
REMARK 500  1 GLU A  29       37.20   -172.89                                   
REMARK 500  1 VAL A  30      171.39    -45.69                                   
REMARK 500  1 SER A  35       52.43    -61.69                                   
REMARK 500  1 ALA A  36       -5.36    -56.84                                   
REMARK 500  1 ASP A  38      -66.72   -156.04                                   
REMARK 500  1 LYS A  39        3.60    -58.72                                   
REMARK 500  1 THR A  40       14.64     35.73                                   
REMARK 500  1 ARG A  41     -116.46   -107.30                                   
REMARK 500  1 VAL A  60      -63.46    -21.68                                   
REMARK 500  1 SER A  67      -27.40    -38.08                                   
REMARK 500  1 GLN A  68     -150.35    -91.29                                   
REMARK 500  1 VAL A  69      153.47     58.72                                   
REMARK 500  1 LYS A  70       89.83   -179.16                                   
REMARK 500  1 ASN A  71       64.11     66.56                                   
REMARK 500  1 VAL A  73      -48.50   -134.30                                   
REMARK 500  1 TYR A  74       34.69    -62.09                                   
REMARK 500  1 LEU A  83       -1.16   -166.69                                   
REMARK 500  1 ASN A  97     -151.59    -71.88                                   
REMARK 500  1 ASN A 103     -143.75    -87.42                                   
REMARK 500  1 ALA A 105     -134.62   -101.78                                   
REMARK 500  1 CYS A 106      -51.81   -154.21                                   
REMARK 500  1 SER A 107       65.40   -165.26                                   
REMARK 500  1 PRO A 132      105.48    -41.30                                   
REMARK 500  1 TRP A 139     -164.70    171.87                                   
REMARK 500  1 GLU A 143      -89.32    -33.74                                   
REMARK 500  1 ASP A 144       56.55   -108.93                                   
REMARK 500  1 ALA A 159        8.91    -67.81                                   
REMARK 500  1 ARG A 160      -82.96   -124.65                                   
REMARK 500  2 SER A   0      -63.71   -146.57                                   
REMARK 500  2 MET A   1     -178.39    -55.53                                   
REMARK 500  2 GLU A   7       79.22     41.02                                   
REMARK 500  2 VAL A   9     -174.75    -61.11                                   
REMARK 500  2 ALA A  10       96.14     48.33                                   
REMARK 500  2 ALA A  11      -62.68   -106.80                                   
REMARK 500  2 PRO A  27     -109.41    -34.00                                   
REMARK 500  2 GLU A  29       47.36   -170.24                                   
REMARK 500  2 SER A  35      -60.33    102.72                                   
REMARK 500  2 LYS A  39      -32.19    -32.38                                   
REMARK 500  2 THR A  40       55.38   -143.28                                   
REMARK 500  2 VAL A  60      -67.34    -16.38                                   
REMARK 500  2 GLN A  68       -8.70    103.20                                   
REMARK 500  2 LYS A  70     -131.22   -110.22                                   
REMARK 500  2 ASN A  71     -135.54     53.68                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     507 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2QPW   RELATED DB: PDB                                   
REMARK 900 X-RAY STRUCTURE OF A SHORTHER CONSTRUCT                              
DBREF  2JV0 A    1   161  UNP    Q13029   PRDM2_HUMAN      1    161             
SEQADV 2JV0 GLY A   -1  UNP  Q13029              EXPRESSION TAG                 
SEQADV 2JV0 SER A    0  UNP  Q13029              EXPRESSION TAG                 
SEQADV 2JV0 ASP A    2  UNP  Q13029    ASN     2 ENGINEERED                     
SEQADV 2JV0 IAS A  141  UNP  Q13029    ASN   141 ENGINEERED                     
SEQRES   1 A  163  GLY SER MET ASP GLN ASN THR THR GLU PRO VAL ALA ALA          
SEQRES   2 A  163  THR GLU THR LEU ALA GLU VAL PRO GLU HIS VAL LEU ARG          
SEQRES   3 A  163  GLY LEU PRO GLU GLU VAL ARG LEU PHE PRO SER ALA VAL          
SEQRES   4 A  163  ASP LYS THR ARG ILE GLY VAL TRP ALA THR LYS PRO ILE          
SEQRES   5 A  163  LEU LYS GLY LYS LYS PHE GLY PRO PHE VAL GLY ASP LYS          
SEQRES   6 A  163  LYS LYS ARG SER GLN VAL LYS ASN ASN VAL TYR MET TRP          
SEQRES   7 A  163  GLU VAL TYR TYR PRO ASN LEU GLY TRP MET CYS ILE ASP          
SEQRES   8 A  163  ALA THR ASP PRO GLU LYS GLY ASN TRP LEU ARG TYR VAL          
SEQRES   9 A  163  ASN TRP ALA CYS SER GLY GLU GLU GLN ASN LEU PHE PRO          
SEQRES  10 A  163  LEU GLU ILE ASN ARG ALA ILE TYR TYR LYS THR LEU LYS          
SEQRES  11 A  163  PRO ILE ALA PRO GLY GLU GLU LEU LEU VAL TRP TYR IAS          
SEQRES  12 A  163  GLY GLU ASP ASN PRO GLU ILE ALA ALA ALA ILE GLU GLU          
SEQRES  13 A  163  GLU ARG ALA SER ALA ARG SER                                  
HET    IAS  A 141      12                                                       
HETNAM     IAS BETA-L-ASPARTIC ACID                                             
HETSYN     IAS L-ASPARTIC ACID                                                  
FORMUL   1  IAS    C4 H7 N O4                                                   
HELIX    1   1 PRO A   19  ARG A   24  1                                   6    
HELIX    2   2 TRP A   98  VAL A  102  5                                   5    
HELIX    3   3 ASN A  145  ALA A  159  1                                  15    
SHEET    1   A 2 ARG A  31  PRO A  34  0                                        
SHEET    2   A 2 ILE A  42  TRP A  45 -1  O  GLY A  43   N  PHE A  33           
SHEET    1   B 3 LYS A  54  PHE A  59  0                                        
SHEET    2   B 3 ALA A 121  THR A 126 -1  O  TYR A 124   N  PHE A  56           
SHEET    3   B 3 PHE A 114  ILE A 118 -1  N  ILE A 118   O  ALA A 121           
SHEET    1   C 3 LYS A  63  LYS A  64  0                                        
SHEET    2   C 3 GLY A  84  ASP A  89 -1  O  CYS A  87   N  LYS A  64           
SHEET    3   C 3 MET A  75  TYR A  80 -1  N  TYR A  80   O  GLY A  84           
SHEET    1   D 2 ASN A 103  TRP A 104  0                                        
SHEET    2   D 2 LEU A 137  VAL A 138  1  O  VAL A 138   N  ASN A 103           
LINK         C   TYR A 140                 N   IAS A 141     1555   1555  1.34  
LINK         CG  IAS A 141                 N   GLY A 142     1555   1555  1.35  
CISPEP   1 GLY A   57    PRO A   58          1         0.43                     
CISPEP   2 GLY A   57    PRO A   58          2         0.74                     
CISPEP   3 GLY A   57    PRO A   58          3        -1.61                     
CISPEP   4 GLY A   57    PRO A   58          4        -0.61                     
CISPEP   5 GLY A   57    PRO A   58          5        -0.56                     
CISPEP   6 GLY A   57    PRO A   58          6        -0.44                     
CISPEP   7 GLY A   57    PRO A   58          7         0.23                     
CISPEP   8 GLY A   57    PRO A   58          8         0.04                     
CISPEP   9 GLY A   57    PRO A   58          9        -1.05                     
CISPEP  10 GLY A   57    PRO A   58         10         3.10                     
CISPEP  11 GLY A   57    PRO A   58         11         0.89                     
CISPEP  12 GLY A   57    PRO A   58         12         0.70                     
CISPEP  13 GLY A   57    PRO A   58         13         0.49                     
CISPEP  14 GLY A   57    PRO A   58         14         0.49                     
CISPEP  15 GLY A   57    PRO A   58         15        -0.57                     
CISPEP  16 GLY A   57    PRO A   58         16         0.68                     
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                                                                             
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