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Entry: 1IYF
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Original site: 1IYF 
HEADER    LIGASE                                  13-AUG-02   1IYF              
TITLE     SOLUTION STRUCTURE OF UBIQUITIN-LIKE DOMAIN OF HUMAN PARKIN           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PARKIN;                                                    
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UBIQUITIN-LIKE DOMAIN;                                     
COMPND   5 EC: 6.3.2.19;                                                        
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 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS;                        
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PGEX6P3                                   
KEYWDS    UBIQUITIN FOLD, RIKEN STRUCTURAL GENOMICS/PROTEOMICS                  
KEYWDS   2 INITIATIVE, RSGI, STRUCTURAL GENOMICS, LIGASE                        
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,S.YOKOYAMA,                 
AUTHOR   2 H.KAWAHARA,H.YOKOSAWA,N.HATTORI,Y.MIZUNO,K.TANAKA,K.KATO,            
AUTHOR   3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)               
REVDAT   2   24-FEB-09 1IYF    1       VERSN                                    
REVDAT   1   25-MAR-03 1IYF    0                                                
JRNL        AUTH   E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,                   
JRNL        AUTH 2 S.YOKOYAMA,S.YAMADA,H.KAWAHARA,H.YOKOSAWA,                   
JRNL        AUTH 3 N.HATTORI,Y.MIZUNO,K.TANAKA,K.KATO                           
JRNL        TITL   PARKIN BINDS THE RPN10 SUBUNIT OF 26S PROTEASOMES            
JRNL        TITL 2 THROUGH ITS UBIQUITIN-LIKE DOMAIN                            
JRNL        REF    EMBO REP.                     V.   4   301 2003              
JRNL        REFN                   ISSN 1469-221X                               
JRNL        PMID   12634850                                                     
JRNL        DOI    10.1038/SJ.EMBOR.EMBOR764                                    
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.1                                              
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL       
REMARK   3  OF 720 RESTRAINTS, 489 ARE NOE-DERIVED DISTANCE CONSTRAINTS,        
REMARK   3  82 DIHEDRAL ANGLE RESTRAINTS, 129 RESIDUAL DIPOLAR COUPLING         
REMARK   3  CONSTRAINTS, 20 DISTANCE RESTRAINTS FOR HYDROGEN BONDS.             
REMARK   4                                                                      
REMARK   4 1IYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-02.                  
REMARK 100 THE RCSB ID CODE IS RCSB005405.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 303; 310                           
REMARK 210  PH                             : 6.0; 6.0                           
REMARK 210  IONIC STRENGTH                 : 0.3; 0.3                           
REMARK 210  PRESSURE                       : 1ATM; 1ATM                         
REMARK 210  SAMPLE CONTENTS                : 0.1MM PARKIN UBIQUITIN-LIKE        
REMARK 210                                   DOMAIN U-15N, 13C; 50MM            
REMARK 210                                   POTASSIUM PHOSPHATE BUFFER;        
REMARK 210                                   0.1MM PARKIN UBIQUITIN-LIKE        
REMARK 210                                   DOMAIN U-15N, 13C; 50MM            
REMARK 210                                   POTASSIUM PHOSPHATE BUFFER         
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY, 3D_        
REMARK 210                                   15N-SEPARATED_NOESY, 2D_1H-        
REMARK 210                                   COUPLED_1H-15N_HSQC                
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ                            
REMARK 210  SPECTROMETER MODEL             : DRX                                
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : XWINNMR 2.6, CNS 1.1               
REMARK 210   METHOD USED                   : DISTANCE GEOMETRY, SIMULATED       
REMARK 210                                   ANNEALING                          
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
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: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR      
REMARK 210  SPECTROSCOPY.                                                       
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-10                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     GLY A    -4                                                      
REMARK 465     PRO A    -3                                                      
REMARK 465     LEU A    -2                                                      
REMARK 465     GLY A    -1                                                      
REMARK 465     SER A     0                                                      
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    ILE A    44     O    HIS A    68              2.10            
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 ASN A   8       69.22    -63.01                                   
REMARK 500  1 HIS A  11      115.51   -160.52                                   
REMARK 500  1 VAL A  17      154.60    177.10                                   
REMARK 500  1 THR A  21      154.39    -37.18                                   
REMARK 500  1 SER A  22      142.73    -18.26                                   
REMARK 500  1 ILE A  23      -39.43    -39.70                                   
REMARK 500  1 VAL A  30      -71.78    -58.46                                   
REMARK 500  1 PRO A  37     -152.24    -65.17                                   
REMARK 500  1 ALA A  38      -70.44   -106.54                                   
REMARK 500  1 LEU A  41     -143.33    -82.67                                   
REMARK 500  1 ALA A  46       36.28     23.62                                   
REMARK 500  1 LEU A  50       87.81     -9.77                                   
REMARK 500  1 VAL A  56     -133.45    -70.66                                   
REMARK 500  1 CYS A  59      -78.66    -81.36                                   
REMARK 500  1 ASP A  60       76.02   -168.73                                   
REMARK 500  2 ASN A   8       68.90    -63.73                                   
REMARK 500  2 VAL A  17      152.40    178.88                                   
REMARK 500  2 THR A  21      150.58    -33.51                                   
REMARK 500  2 SER A  22      142.99    -17.30                                   
REMARK 500  2 ILE A  23      -39.99    -39.69                                   
REMARK 500  2 VAL A  30      -73.41    -58.78                                   
REMARK 500  2 PRO A  37     -148.87    -66.30                                   
REMARK 500  2 ALA A  38      -68.02   -105.31                                   
REMARK 500  2 GLN A  40      -76.31    -53.20                                   
REMARK 500  2 LEU A  41     -138.36    -84.74                                   
REMARK 500  2 ALA A  46       34.90     26.03                                   
REMARK 500  2 LEU A  50       89.51    -14.52                                   
REMARK 500  2 VAL A  56     -133.53    -82.29                                   
REMARK 500  2 CYS A  59      -76.99    -96.71                                   
REMARK 500  2 ASP A  60       76.65   -169.94                                   
REMARK 500  3 ASN A   8       69.39    -63.91                                   
REMARK 500  3 VAL A  17      157.59    175.41                                   
REMARK 500  3 THR A  21      153.69    -35.19                                   
REMARK 500  3 SER A  22      144.27    -16.62                                   
REMARK 500  3 VAL A  30      -73.53    -61.88                                   
REMARK 500  3 PRO A  37     -147.57    -67.04                                   
REMARK 500  3 ALA A  38      -69.82   -105.96                                   
REMARK 500  3 GLN A  40      -77.32    -49.02                                   
REMARK 500  3 LEU A  41     -124.71    -81.94                                   
REMARK 500  3 ALA A  46       37.86     26.87                                   
REMARK 500  3 LEU A  50      107.64    -25.05                                   
REMARK 500  3 VAL A  56     -135.01    -82.26                                   
REMARK 500  3 CYS A  59      -79.10   -106.22                                   
REMARK 500  3 ASP A  60       76.46   -165.39                                   
REMARK 500  4 ASN A   8       68.53    -64.13                                   
REMARK 500  4 VAL A  17      154.71    178.99                                   
REMARK 500  4 THR A  21      152.42    -34.35                                   
REMARK 500  4 SER A  22      143.14    -18.87                                   
REMARK 500  4 VAL A  30      -74.01    -59.05                                   
REMARK 500  4 PRO A  37     -145.19    -68.20                                   
REMARK 500  4 ALA A  38      -65.68   -104.58                                   
REMARK 500  4 GLN A  40      -85.26    -43.95                                   
REMARK 500  4 LEU A  41     -113.89    -94.19                                   
REMARK 500  4 ALA A  46       38.02     25.21                                   
REMARK 500  4 LEU A  50       87.94    -10.89                                   
REMARK 500  4 VAL A  56     -134.36    -78.63                                   
REMARK 500  4 CYS A  59      -78.17    -96.09                                   
REMARK 500  4 ASP A  60       76.67   -169.27                                   
REMARK 500  5 ASN A   8       71.45    -59.28                                   
REMARK 500  5 VAL A  17      152.73    178.86                                   
REMARK 500  5 THR A  21      154.32    -35.34                                   
REMARK 500  5 SER A  22      142.79    -18.12                                   
REMARK 500  5 VAL A  30      -75.01    -57.12                                   
REMARK 500  5 PRO A  37     -148.35    -70.03                                   
REMARK 500  5 GLN A  40       92.59    -56.27                                   
REMARK 500  5 LEU A  41     -161.16    -69.90                                   
REMARK 500  5 ARG A  42       44.74     70.58                                   
REMARK 500  5 ALA A  46       35.79     27.41                                   
REMARK 500  5 LEU A  50       88.24    -14.14                                   
REMARK 500  5 VAL A  56     -136.88    -82.89                                   
REMARK 500  5 CYS A  59      -78.33   -104.08                                   
REMARK 500  5 ASP A  60       77.60   -167.04                                   
REMARK 500  6 ASN A   8       71.53    -66.38                                   
REMARK 500  6 SER A   9     -160.77   -163.93                                   
REMARK 500  6 SER A  10      177.09    -49.41                                   
REMARK 500  6 THR A  21      153.96    -32.79                                   
REMARK 500  6 SER A  22      143.95    -20.69                                   
REMARK 500  6 VAL A  30      -74.01    -67.03                                   
REMARK 500  6 PRO A  37     -142.36    -66.62                                   
REMARK 500  6 ALA A  38      -73.07   -104.68                                   
REMARK 500  6 LEU A  41     -138.74    -83.20                                   
REMARK 500  6 ALA A  46       35.84     24.25                                   
REMARK 500  6 LEU A  50       97.09    -21.46                                   
REMARK 500  6 VAL A  56     -137.35    -83.81                                   
REMARK 500  6 CYS A  59      -77.47   -101.45                                   
REMARK 500  6 ASP A  60       78.53   -165.68                                   
REMARK 500  6 VAL A  70       74.31   -104.09                                   
REMARK 500  7 ASN A   8       70.44    -58.43                                   
REMARK 500  7 VAL A  17     -169.33   -167.37                                   
REMARK 500  7 THR A  21      175.92    -40.19                                   
REMARK 500  7 SER A  22      154.93    -40.18                                   
REMARK 500  7 GLN A  25      -71.30    -58.82                                   
REMARK 500  7 VAL A  30      -74.57    -62.09                                   
REMARK 500  7 PRO A  37     -140.42    -65.48                                   
REMARK 500  7 ALA A  38      -74.89   -110.80                                   
REMARK 500  7 LEU A  41     -136.25    -91.83                                   
REMARK 500  7 ALA A  46       31.85     77.21                                   
REMARK 500  7 LEU A  50       82.16    -14.64                                   
REMARK 500  7 VAL A  56     -129.49    -51.65                                   
REMARK 500  7 CYS A  59      -72.15    -63.73                                   
REMARK 500  7 ASP A  60       74.94   -166.40                                   
REMARK 500  7 GLN A  71       60.51   -118.57                                   
REMARK 500  8 ASN A   8       72.72    -64.46                                   
REMARK 500  8 SER A   9     -161.15   -163.76                                   
REMARK 500  8 SER A  10      175.59    -49.38                                   
REMARK 500  8 VAL A  17      156.03    179.61                                   
REMARK 500  8 THR A  21      154.75    -33.17                                   
REMARK 500  8 SER A  22      143.67    -20.63                                   
REMARK 500  8 VAL A  30      -72.48    -55.42                                   
REMARK 500  8 PRO A  37     -149.79    -66.72                                   
REMARK 500  8 ALA A  38      -69.90   -105.83                                   
REMARK 500  8 GLN A  40      -73.01    -52.26                                   
REMARK 500  8 LEU A  41     -135.03    -82.13                                   
REMARK 500  8 ALA A  46       37.91     22.53                                   
REMARK 500  8 LEU A  50       97.46    -22.70                                   
REMARK 500  8 VAL A  56     -133.47    -81.81                                   
REMARK 500  8 CYS A  59      -78.03    -95.90                                   
REMARK 500  8 ASP A  60       76.01   -168.41                                   
REMARK 500  9 ASN A   8       71.92    -66.76                                   
REMARK 500  9 SER A   9     -159.43   -163.91                                   
REMARK 500  9 SER A  10      175.80    -48.95                                   
REMARK 500  9 VAL A  17     -166.43   -167.84                                   
REMARK 500  9 THR A  21      169.45    -36.14                                   
REMARK 500  9 SER A  22      148.20    -33.88                                   
REMARK 500  9 VAL A  30      -75.75    -57.67                                   
REMARK 500  9 PRO A  37     -147.30    -63.51                                   
REMARK 500  9 ALA A  38      -77.78   -108.79                                   
REMARK 500  9 GLN A  40      -71.10    -46.43                                   
REMARK 500  9 LEU A  41     -138.60    -90.12                                   
REMARK 500  9 ALA A  46       28.69     40.61                                   
REMARK 500  9 VAL A  56     -140.55    -79.88                                   
REMARK 500  9 CYS A  59      -73.67    -84.72                                   
REMARK 500  9 ASP A  60       84.14   -170.66                                   
REMARK 500 10 ASN A   8      178.09    -42.76                                   
REMARK 500 10 SER A   9       79.86    -49.17                                   
REMARK 500 10 VAL A  17      156.35    176.39                                   
REMARK 500 10 THR A  21      151.27    -34.09                                   
REMARK 500 10 SER A  22      143.92    -17.96                                   
REMARK 500 10 VAL A  30      -74.09    -62.53                                   
REMARK 500 10 PRO A  37     -144.20    -66.93                                   
REMARK 500 10 ALA A  38      -68.05   -107.09                                   
REMARK 500 10 GLN A  40      -81.96    -48.53                                   
REMARK 500 10 LEU A  41     -126.18    -87.33                                   
REMARK 500 10 ALA A  46       37.89     26.62                                   
REMARK 500 10 LEU A  50      103.14    -21.66                                   
REMARK 500 10 VAL A  56     -132.82    -80.75                                   
REMARK 500 10 CYS A  59      -78.24    -97.21                                   
REMARK 500 10 ASP A  60       76.39   -168.68                                   
REMARK 500 10 GLN A  71       70.69   -117.39                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5500   RELATED DB: BMRB                                  
REMARK 900 5500 IS CHEMICAL SHIFT                                               
REMARK 900 RELATED ID: MY_001000012.1   RELATED DB: TARGETDB                    
DBREF  1IYF A    1    76  UNP    O60260   PRKN2_HUMAN      1     76             
SEQADV 1IYF GLY A   -4  UNP  O60260              CLONING ARTIFACT               
SEQADV 1IYF PRO A   -3  UNP  O60260              CLONING ARTIFACT               
SEQADV 1IYF LEU A   -2  UNP  O60260              CLONING ARTIFACT               
SEQADV 1IYF GLY A   -1  UNP  O60260              CLONING ARTIFACT               
SEQADV 1IYF SER A    0  UNP  O60260              CLONING ARTIFACT               
SEQRES   1 A   81  GLY PRO LEU GLY SER MET ILE VAL PHE VAL ARG PHE ASN          
SEQRES   2 A   81  SER SER HIS GLY PHE PRO VAL GLU VAL ASP SER ASP THR          
SEQRES   3 A   81  SER ILE PHE GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN          
SEQRES   4 A   81  GLY VAL PRO ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY          
SEQRES   5 A   81  LYS GLU LEU ARG ASN ASP TRP THR VAL GLN ASN CYS ASP          
SEQRES   6 A   81  LEU ASP GLN GLN SER ILE VAL HIS ILE VAL GLN ARG PRO          
SEQRES   7 A   81  TRP ARG LYS                                                  
HELIX    1   1 SER A   22  GLN A   34  1                                  13    
HELIX    2   2 VAL A   56  LEU A   61  1                                   6    
SHEET    1   A 5 HIS A  11  VAL A  15  0                                        
SHEET    2   A 5 ILE A   2  PHE A   7 -1  N  VAL A   5   O  PHE A  13           
SHEET    3   A 5 GLN A  64  VAL A  70  1  O  ILE A  69   N  ARG A   6           
SHEET    4   A 5 ARG A  42  PHE A  45 -1  N  ARG A  42   O  VAL A  70           
SHEET    5   A 5 LYS A  48  GLU A  49 -1  O  LYS A  48   N  PHE A  45           
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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