HEADER    LIGASE                                  12-JAN-12   2RSD              
TITLE     SOLUTION STRUCTURE OF THE PLANT HOMEODOMAIN (PHD) OF THE E3 SUMO      
TITLE    2 LIGASE SIZ1 FROM RICE                                                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: E3 SUMO-PROTEIN LIGASE SIZ1;                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: PLANT HOMEODOMAIN, UNP RESIDUES 107-172;                   
COMPND   5 EC: 6.3.2.-;                                                         
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP;                    
SOURCE   3 ORGANISM_COMMON: JAPANESE RICE;                                      
SOURCE   4 ORGANISM_TAXID: 39947;                                               
SOURCE   5 GENE: SIZ1, OS05G0125000, LOC_OS05G03430, OSJNBB0079L11.3;           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE  10 EXPRESSION_SYSTEM_VECTOR: PGEX-4T-3                                  
KEYWDS    E3 SUMO LIGASE, PLANT HOMEODOMAIN (PHD), HISTONE BINDING, LIGASE      
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    H.SHINDO,W.TSUCHIYA,R.SUZUKI,T.YAMAZAKI                               
REVDAT   3   15-MAY-24 2RSD    1       REMARK                                   
REVDAT   2   14-JUN-23 2RSD    1       REMARK SEQADV LINK                       
REVDAT   1   15-AUG-12 2RSD    0                                                
JRNL        AUTH   H.SHINDO,R.SUZUKI,W.TSUCHIYA,M.TAICHI,Y.NISHIUCHI,T.YAMAZAKI 
JRNL        TITL   PHD FINGER OF THE SUMO LIGASE SIZ/PIAS FAMILY IN RICE        
JRNL        TITL 2 REVEALS SPECIFIC BINDING FOR METHYLATED HISTONE H3 AT LYSINE 
JRNL        TITL 3 4 AND ARGININE 2                                             
JRNL        REF    FEBS LETT.                    V. 586  1783 2012              
JRNL        REFN                   ISSN 0014-5793                               
JRNL        PMID   22626555                                                     
JRNL        DOI    10.1016/J.FEBSLET.2012.04.063                                
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : XWINNMR 3.1, CYANA 2.1                               
REMARK   3   AUTHORS     : BRUKER BIOSPIN (XWINNMR), GUNTERT, MUMENTHALER AND   
REMARK   3                 WUTHRICH (CYANA)                                     
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2RSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-12.                  
REMARK 100 THE DEPOSITION ID IS D_1000150226.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 7.0                                
REMARK 210  IONIC STRENGTH                 : NULL                               
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.5-1.0 MM [U-13C; U-15N] OSSIZ1   
REMARK 210                                   -PHD-1, 1.0-2.0 MM ZINC ION-2,     
REMARK 210                                   100 MM SODIUM CHLORIDE-3, 10 MM    
REMARK 210                                   POTASSIUM PHOSPHATE-4, 5 MM DTT-   
REMARK 210                                   5, 100% D2O; 0.5-1.0 MM [U-13C;    
REMARK 210                                   U-15N] OSSIZ1-PHD-6, 1.0-2.0 MM    
REMARK 210                                   ZINC ION-7, 100 MM SODIUM          
REMARK 210                                   CHLORIDE-8, 10 MM POTASSIUM        
REMARK 210                                   PHOSPHATE-9, 5 MM DTT-10, 92%      
REMARK 210                                   H2O/8% D2O                         
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC;    
REMARK 210                                   3D CBCA(CO)NH; 3D HNCO; 3D HNCA;   
REMARK 210                                   3D HCABGCO; 3D HCCH-COSY; 3D 15N-  
REMARK 210                                   SEPARATED NOESY-HSQC; 3D 13C/15N-  
REMARK 210                                   SEPARATED NOESY-HSQC; 4D 13C/13C-  
REMARK 210                                   SEPARATED NOESY-HSQC               
REMARK 210  SPECTROMETER FIELD STRENGTH    : 750 MHZ                            
REMARK 210  SPECTROMETER MODEL             : DMX                                
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE RELEASED AT FEB 10,        
REMARK 210                                   2006, SPARKY 3.113, CYANA 2.1,     
REMARK 210                                   TALOS+ 1.01F, AQUA 3.2,            
REMARK 210                                   PROCHECKNMR 3.5.4                  
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS             
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LEAST          
REMARK 210                                   RESTRAINT VIOLATIONS               
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: 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 106      -57.37   -160.33                                   
REMARK 500  1 THR A 122       31.39    -94.23                                   
REMARK 500  1 ASN A 125     -169.25    -70.48                                   
REMARK 500  1 CYS A 136      -59.66   -123.09                                   
REMARK 500  1 CYS A 163     -178.69    -56.07                                   
REMARK 500  2 SER A 106      -69.28     72.10                                   
REMARK 500  2 ASP A 107       32.27    -96.50                                   
REMARK 500  2 PHE A 109       92.22    -69.52                                   
REMARK 500  2 THR A 122       31.18    -94.49                                   
REMARK 500  2 ASN A 125     -169.02    -69.03                                   
REMARK 500  2 CYS A 136      -60.83   -130.92                                   
REMARK 500  2 CYS A 163     -175.89    -57.57                                   
REMARK 500  3 THR A 122       31.41    -94.29                                   
REMARK 500  3 ASN A 125     -169.97    -59.86                                   
REMARK 500  3 CYS A 136      -61.30   -128.88                                   
REMARK 500  3 CYS A 163     -176.07    -57.59                                   
REMARK 500  4 SER A 106      -42.66   -173.07                                   
REMARK 500  4 SER A 108      -35.62   -178.13                                   
REMARK 500  4 PHE A 109       92.23    -67.63                                   
REMARK 500  4 THR A 122       31.88    -94.36                                   
REMARK 500  4 ASN A 125     -169.63    -60.14                                   
REMARK 500  4 CYS A 136      -58.54   -125.84                                   
REMARK 500  4 CYS A 163     -176.37    -57.21                                   
REMARK 500  5 SER A 106       51.99    -95.58                                   
REMARK 500  5 THR A 122       31.33    -93.99                                   
REMARK 500  5 ASN A 125     -169.10    -69.46                                   
REMARK 500  5 CYS A 136      -59.92   -127.75                                   
REMARK 500  5 GLU A 153     -169.82    -75.68                                   
REMARK 500  5 CYS A 163     -175.42    -57.63                                   
REMARK 500  6 SER A 108       47.08   -166.43                                   
REMARK 500  6 THR A 122       31.22    -94.54                                   
REMARK 500  6 ASN A 125     -168.43    -70.06                                   
REMARK 500  6 CYS A 136      -59.14   -124.49                                   
REMARK 500  6 GLU A 153     -169.86    -69.19                                   
REMARK 500  6 ALA A 155      165.27    -48.64                                   
REMARK 500  6 CYS A 163     -177.28    -56.99                                   
REMARK 500  7 SER A 106      -69.26     72.13                                   
REMARK 500  7 SER A 108       46.80   -152.29                                   
REMARK 500  7 VAL A 124       89.94    -65.37                                   
REMARK 500  7 ASN A 125     -168.72    -60.59                                   
REMARK 500  7 CYS A 136      -60.05   -128.12                                   
REMARK 500  7 CYS A 163     -175.82    -57.45                                   
REMARK 500  8 SER A 106       39.46   -169.70                                   
REMARK 500  8 THR A 122       31.97    -94.55                                   
REMARK 500  8 ASN A 125     -169.74    -60.08                                   
REMARK 500  8 CYS A 136      -58.74   -125.53                                   
REMARK 500  8 GLU A 153     -169.69    -76.04                                   
REMARK 500  8 CYS A 163     -175.30    -57.64                                   
REMARK 500  9 SER A 106       70.63     52.78                                   
REMARK 500  9 THR A 122       31.11    -94.03                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     112 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 901  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 117   SG                                                     
REMARK 620 2 CYS A 119   SG  101.0                                              
REMARK 620 3 HIS A 141   ND1 112.1  96.7                                        
REMARK 620 4 CYS A 144   SG   98.0 130.7 117.2                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 902  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 131   SG                                                     
REMARK 620 2 CYS A 136   SG  126.3                                              
REMARK 620 3 CYS A 163   SG  131.6  90.0                                        
REMARK 620 4 CYS A 166   SG   95.5  93.8 114.6                                  
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 901                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 11469   RELATED DB: BMRB                                 
DBREF  2RSD A  107   172  UNP    Q6L4L4   SIZ1_ORYSJ     107    172             
SEQADV 2RSD GLY A  105  UNP  Q6L4L4              EXPRESSION TAG                 
SEQADV 2RSD SER A  106  UNP  Q6L4L4              EXPRESSION TAG                 
SEQRES   1 A   68  GLY SER ASP SER PHE GLN PRO GLU ALA LYS VAL ARG CYS          
SEQRES   2 A   68  ILE CYS SER SER THR MET VAL ASN ASP SER MET ILE GLN          
SEQRES   3 A   68  CYS GLU ASP GLN ARG CYS GLN VAL TRP GLN HIS LEU ASN          
SEQRES   4 A   68  CYS VAL LEU ILE PRO ASP LYS PRO GLY GLU SER ALA GLU          
SEQRES   5 A   68  VAL PRO PRO VAL PHE TYR CYS GLU LEU CYS ARG LEU SER          
SEQRES   6 A   68  ARG ALA ASP                                                  
HET     ZN  A 901       1                                                       
HET     ZN  A 902       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    2(ZN 2+)                                                     
HELIX    1   1 CYS A  163  ALA A  171  1                                   9    
SHEET    1   A 3 LYS A 114  VAL A 115  0                                        
SHEET    2   A 3 VAL A 138  HIS A 141  1  O  TRP A 139   N  LYS A 114           
SHEET    3   A 3 MET A 128  GLN A 130 -1  N  ILE A 129   O  GLN A 140           
LINK         SG  CYS A 117                ZN    ZN A 901     1555   1555  2.42  
LINK         SG  CYS A 119                ZN    ZN A 901     1555   1555  2.32  
LINK         SG  CYS A 131                ZN    ZN A 902     1555   1555  2.42  
LINK         SG  CYS A 136                ZN    ZN A 902     1555   1555  2.54  
LINK         ND1 HIS A 141                ZN    ZN A 901     1555   1555  2.07  
LINK         SG  CYS A 144                ZN    ZN A 901     1555   1555  2.41  
LINK         SG  CYS A 163                ZN    ZN A 902     1555   1555  2.45  
LINK         SG  CYS A 166                ZN    ZN A 902     1555   1555  2.41  
SITE     1 AC1  4 CYS A 117  CYS A 119  HIS A 141  CYS A 144                    
SITE     1 AC2  5 CYS A 131  CYS A 136  VAL A 138  CYS A 163                    
SITE     2 AC2  5 CYS A 166                                                     
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