HEADER    UBIQUITIN                               22-DEC-04   2BGF              
TITLE     NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL SHIFT       
TITLE    2 PERTURBATION DATA TOGETHER WITH RDCS AND 15N-RELAXATION DATA         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DI-UBIQUITIN;                                              
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 SYNONYM: UBIQUITIN;                                                  
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 OTHER_DETAILS: ISOPEPTIDE BOND BETWEEN GLY76A AND LYS48B             
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                                         
KEYWDS    PROTEASOME, DEGRADATION, UBIQUITIN, POLYUBIQUITIN                     
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    A.D.J.VAN DIJK,D.FUSHMAN,A.M.J.J.BONVIN                               
REVDAT   3   15-MAY-24 2BGF    1       REMARK                                   
REVDAT   2   24-FEB-09 2BGF    1       VERSN                                    
REVDAT   1   31-AUG-05 2BGF    0                                                
JRNL        AUTH   A.D.J.VAN DIJK,D.FUSHMAN,A.M.J.J.BONVIN                      
JRNL        TITL   VARIOUS STRATEGIES OF USING RESIDUAL DIPOLAR COUPLINGS IN    
JRNL        TITL 2 NMR-DRIVEN PROTEIN DOCKING: APPLICATION TO LYS48-LINKED      
JRNL        TITL 3 DI-UBIQUITIN AND VALIDATION AGAINST 15N-RELAXATION DATA      
JRNL        REF    PROTEINS: STRUCT., FUNCT.,    V.  60   367 2005              
JRNL        REF  2 BIOINF.                                                      
JRNL        REFN                   ISSN 0887-3585                               
JRNL        PMID   15937902                                                     
JRNL        DOI    10.1002/PROT.20476                                           
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   R.VARADAN,O.WALKER,C.PICKART,D.FUSHMAN                       
REMARK   1  TITL   STRUCTURAL PROPERTIES OF POLYUBIQUITIN CHAINS IN SOLUTION    
REMARK   1  REF    J.MOL.BIOL.                   V. 324   637 2002              
REMARK   1  REFN                   ISSN 0022-2836                               
REMARK   1  PMID   12460567                                                     
REMARK   1  DOI    10.1016/S0022-2836(02)01198-1                                
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : HADDOCK                                              
REMARK   3   AUTHORS     : DOMINGUEZ, BOELENS,BONVIN                            
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: REFINEMENT IS DONE IN EXPLICIT SOLVENT.   
REMARK   3  REFINEMENT AND STRUCTURE CALCULATION DETAILS CAN BE FOUND IN        
REMARK   3  DOMINGUEZ ET AL, JACS 2003, 125, 173                                
REMARK   4                                                                      
REMARK   4 2BGF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-04.                  
REMARK 100 THE DEPOSITION ID IS D_1290022088.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298.0                              
REMARK 210  PH                             : 6.8                                
REMARK 210  IONIC STRENGTH                 : 20                                 
REMARK 210  PRESSURE                       : 1.0 ATM                            
REMARK 210  SAMPLE CONTENTS                : 90% WATER/10% D20                  
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : HSQC; TOCSY                        
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : OTHER                              
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : HADDOCK                            
REMARK 210   METHOD USED                   : HADDOCK                            
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 200                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : LOWEST ENERGY STRUCTURES OF        
REMARK 210                                   LOWEST ENERGY CLUSTER              
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING CHEMICAL     
REMARK 210  SHIFT PERTURBATION DATA AS AMBIGUOUS INTERACTION RESTRAINTS AND     
REMARK 210  RESIDUAL DIPOLAR COUPLINGS BOTH AS DIRECT RESTRAINTS (SANI) AND     
REMARK 210  INTERVECTOR PROJECTION ANGLE RESTRAINTS (VEAN). STRUCTURAL          
REMARK 210  CHARACTERISTICS OF ENSEMBLE OF 10 BEST: AVERAGE (STANDARD           
REMARK 210  DEVIATION) INTERMOLECULAR ENERGIES RAMACHANDRAN ANALYSIS:           
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: DIMERIC                           
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B                                  
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 400                                                                      
REMARK 400 COMPOUND                                                             
REMARK 400 FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF             
REMARK 400  CELLULAR PROTEINS, MAINTENANCE OF CHROMATIN STRUCTURE,              
REMARK 400  REGULATION OF GENE EXPRESSION, STRESS RESPONSE, AND                 
REMARK 400  RIBOSOME BIOGENESIS                                                 
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                                                                      
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 GLU A  16       79.95   -105.17                                   
REMARK 500  1 LYS A  33      -83.42    -80.90                                   
REMARK 500  1 ALA A  46       -2.29     65.45                                   
REMARK 500  1 GLN A  62     -167.04   -119.23                                   
REMARK 500  1 GLU A  64       12.26     59.83                                   
REMARK 500  1 LYS B  11      140.38   -175.53                                   
REMARK 500  1 LYS B  33      -76.46   -100.94                                   
REMARK 500  2 LYS A  33      -80.51    -81.79                                   
REMARK 500  2 ALA A  46       -9.34     69.20                                   
REMARK 500  2 LYS B  33      -69.20   -108.80                                   
REMARK 500  3 GLU A  16       77.00   -112.36                                   
REMARK 500  3 LYS A  33      -83.72    -84.78                                   
REMARK 500  3 LEU A  67     -164.70   -113.92                                   
REMARK 500  3 LYS B  33      -76.21   -107.33                                   
REMARK 500  4 GLU A  16       77.83   -105.40                                   
REMARK 500  4 LYS A  33      -79.17    -80.93                                   
REMARK 500  4 GLN A  62     -163.91   -123.43                                   
REMARK 500  4 GLU A  64       14.44     56.51                                   
REMARK 500  4 ALA B  46       17.30     57.58                                   
REMARK 500  4 GLN B  62     -161.45   -110.16                                   
REMARK 500  5 LYS A  33      -80.98    -84.09                                   
REMARK 500  5 GLN A  62     -159.47   -127.23                                   
REMARK 500  5 LYS B  33      -73.54   -111.25                                   
REMARK 500  5 LEU B  73     -109.12    -80.53                                   
REMARK 500  5 ARG B  74      -36.52   -170.11                                   
REMARK 500  6 GLU A  16       78.62   -114.41                                   
REMARK 500  6 LYS A  33      -83.37    -76.60                                   
REMARK 500  6 GLN A  62     -165.24   -128.22                                   
REMARK 500  6 ARG A  72       57.64    -90.39                                   
REMARK 500  6 LYS B  33      -66.94   -108.94                                   
REMARK 500  6 GLN B  62     -165.57   -103.43                                   
REMARK 500  7 GLU A  16       76.47   -103.55                                   
REMARK 500  7 LYS A  33      -84.80    -79.60                                   
REMARK 500  7 GLU A  64       10.15     58.33                                   
REMARK 500  7 ARG A  72       64.67   -112.26                                   
REMARK 500  7 LYS B  33      -76.92   -108.60                                   
REMARK 500  7 GLN B  62     -167.84   -105.01                                   
REMARK 500  8 LYS A  33      -83.02    -81.68                                   
REMARK 500  8 LYS B  33      -68.22   -108.96                                   
REMARK 500  8 ASN B  60       32.62     71.71                                   
REMARK 500  8 ARG B  74       62.25   -119.42                                   
REMARK 500  9 LYS A  33      -77.61    -85.35                                   
REMARK 500  9 GLN A  62     -159.10   -136.98                                   
REMARK 500  9 LEU A  73     -164.66   -105.75                                   
REMARK 500  9 GLN B  62     -164.76   -105.08                                   
REMARK 500 10 LYS A  33      -78.54    -90.03                                   
REMARK 500 10 ALA A  46      -43.67     72.81                                   
REMARK 500 10 GLN A  62     -166.14   -118.18                                   
REMARK 500 10 GLU A  64       13.04     58.95                                   
REMARK 500 10 LEU A  73      -83.15    -82.14                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      54 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1AAR   RELATED DB: PDB                                   
REMARK 900 DI-UBIQUITIN                                                         
REMARK 900 RELATED ID: 1E0Q   RELATED DB: PDB                                   
REMARK 900 MUTANT PEPTIDE FROM THE FIRST N-TERMINAL 17 AMINO-ACID OF UBIQUITIN  
REMARK 900 RELATED ID: 1P3Q   RELATED DB: PDB                                   
REMARK 900 MECHANISM OF UBIQUITIN RECOGNITION BY THE CUE DOMAIN OF VPS9         
REMARK 900 RELATED ID: 1UZX   RELATED DB: PDB                                   
REMARK 900 A COMPLEX OF THE VPS23 UEV WITH UBIQUITIN                            
DBREF  2BGF A    1    76  UNP    P62988   UBIQ_HUMAN       1     76             
DBREF  2BGF B    1    76  UNP    P62988   UBIQ_HUMAN       1     76             
SEQRES   1 A   76  MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE          
SEQRES   2 A   76  THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL          
SEQRES   3 A   76  LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP          
SEQRES   4 A   76  GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP          
SEQRES   5 A   76  GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER          
SEQRES   6 A   76  THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY                  
SEQRES   1 B   76  MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE          
SEQRES   2 B   76  THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL          
SEQRES   3 B   76  LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP          
SEQRES   4 B   76  GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP          
SEQRES   5 B   76  GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER          
SEQRES   6 B   76  THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY                  
HELIX    1   1 THR A   22  GLU A   34  1                                  13    
HELIX    2   2 PRO A   37  ASP A   39  5                                   3    
HELIX    3   3 LEU A   56  ASN A   60  5                                   5    
HELIX    4   4 THR B   22  GLU B   34  1                                  13    
HELIX    5   5 PRO B   37  ASP B   39  5                                   3    
HELIX    6   6 LEU B   56  ASN B   60  5                                   5    
SHEET    1  AA 5 LYS A  11  GLU A  16  0                                        
SHEET    2  AA 5 GLN A   2  THR A   7 -1  O  ILE A   3   N  LEU A  15           
SHEET    3  AA 5 THR A  66  LEU A  71  1  O  LEU A  67   N  LYS A   6           
SHEET    4  AA 5 GLN A  41  PHE A  45 -1  O  ARG A  42   N  VAL A  70           
SHEET    5  AA 5 LYS A  48  GLN A  49 -1  O  LYS A  48   N  PHE A  45           
SHEET    1  BA 5 THR B  12  GLU B  16  0                                        
SHEET    2  BA 5 GLN B   2  THR B   7 -1  O  ILE B   3   N  LEU B  15           
SHEET    3  BA 5 THR B  66  LEU B  71  1  O  LEU B  67   N  LYS B   6           
SHEET    4  BA 5 GLN B  41  PHE B  45 -1  O  ARG B  42   N  VAL B  70           
SHEET    5  BA 5 LYS B  48  GLN B  49 -1  O  LYS B  48   N  PHE B  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