PDB Short entry for 2PEA
HEADER    SIGNALING PROTEIN                       02-APR-07   2PEA              
TITLE     NMR BASED STRUCTURE OF THE CLOSED CONFORMATION OF LYS48-              
TITLE    2 LINKED DI-UBIQUITIN USING EXPERIMENTAL GLOBAL ROTATIONAL             
TITLE    3 DIFFUSION TENSOR FROM NMR RELAXATION MEASUREMENTS                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: UBIQUITIN;                                                 
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 SYNONYM: UBIQUITIN;                                                  
COMPND   5 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                                         
KEYWDS    UBIQUITIN, LYS48-LINKED DI-UBIQUITIN, POLYUBIQUITIN,                  
KEYWDS   2 SIGNALING PROTEIN                                                    
EXPDTA    SOLUTION NMR                                                          
AUTHOR    Y.RYABOV,D.FUSHMAN                                                    
REVDAT   2   24-FEB-09 2PEA    1       VERSN                                    
REVDAT   1   10-JUL-07 2PEA    0                                                
JRNL        AUTH   Y.RYABOV,D.FUSHMAN                                           
JRNL        TITL   STRUCTURAL ASSEMBLY OF MULTIDOMAIN PROTEINS AND              
JRNL        TITL 2 PROTEIN COMPLEXES GUIDED BY THE OVERALL ROTATIONAL           
JRNL        TITL 3 DIFFUSION TENSOR.                                            
JRNL        REF    J.AM.CHEM.SOC.                V. 129  7894 2007              
JRNL        REFN                   ISSN 0002-7863                               
JRNL        PMID   17550252                                                     
JRNL        DOI    10.1021/JA071185D                                            
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   Y.RYABOV,C.GERAGHTY,A.VARSHNEY,D.FUSHMAN                     
REMARK   1  TITL   AN EFFICIENT COMPUTATIONAL METHOD FOR PREDICTING             
REMARK   1  TITL 2 ROTATIONAL DIFFUSION TENSORS OF GLOBULAR PROTEINS            
REMARK   1  TITL 3 USING AN ELLIPSOID REPRESENTATION.                           
REMARK   1  REF    J.AM.CHEM.SOC.                V. 128 15432 2006              
REMARK   1  REFN                   ISSN 0002-7863                               
REMARK   1  PMID   17132010                                                     
REMARK   1  DOI    10.1021/JA062715T                                            
REMARK   1 REFERENCE 2                                                          
REMARK   1  AUTH   Y.RYABOV,D.FUSHMAN                                           
REMARK   1  TITL   A MODEL OF INTERDOMAIN MOBILITY IN A MULTIDOMAIN             
REMARK   1  TITL 2 PROTEIN                                                      
REMARK   1  REF    J.AM.CHEM.SOC.                V. 129  3315 2007              
REMARK   1  REFN                   ISSN 0002-7863                               
REMARK   1  PMID   17319663                                                     
REMARK   1  DOI    10.1021/JA067667R                                            
REMARK   1 REFERENCE 3                                                          
REMARK   1  AUTH   R.VARADAN,O.WALKER,C.PICKART,D.FUSHMAN                       
REMARK   1  TITL   STRUCTURAL PROPERTIES OF POLYUBIQUITIN CHAINS IN             
REMARK   1  TITL 2 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     : ELM                                                  
REMARK   3   AUTHORS     : Y.RYABOV, D.FUSHMAN                                  
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: THE STRUCTURE WAS DETERMINED WITH         
REMARK   3  PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI-       
REMARK   3  UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND        
REMARK   3  POSITIONING OF THE INDIVIDUAL UBIQUITIN DOMAINS WITHIN THE          
REMARK   3  MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY          
REMARK   3  ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF       
REMARK   3  THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN         
REMARK   3  POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY           
REMARK   3  TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED      
REMARK   3  ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS. FOR EACH UBIQUITIN       
REMARK   3  DOMAIN THE STRUCTURE OF THE FIRST CONFORMER OF PDB ENTRY 1D3Z       
REMARK   3  WAS ASSUMED. THE DEPOSITED CONFORMATION REPRESENTS ONE OF THE       
REMARK   3  TWO EXPERIMENTALLY DETECTABLE CONFORMATIONS OF DI-UBIQUITIN AT      
REMARK   3  PH 6.8. THE OCCUPATION PROBABILITY OF THIS CONFORMATION IS          
REMARK   3  APPROXIMATELY 90%. CHAIN A CORRESPONDS TO UBIQUITIN DOMAIN          
REMARK   3  THAT HAS A FREE C-TERMINUS IN DI-UBIQUITIN. CHAIN B                 
REMARK   3  CORRESPONDS TO UBIQUITIN DOMAIN THAT IN DI-UBIQUITIN IS LINKED      
REMARK   3  VIA AN ISOPEPTIDE BOND BETWEEN ITS C- TERMINAL GLY76 AND LYS48      
REMARK   3  OF CHAIN A. THE ISOPEPTIDE BOND WAS PRESENT IN THE DI-              
REMARK   3  UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER, BECAUSE THIS             
REMARK   3  STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION AND                 
REMARK   3  TRANSLATION AND NO CONSTRAINTS REPRESENTING THE INTERDOMAIN         
REMARK   3  LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE IS NOT PRESENT        
REMARK   3  IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH UBIQUTIN DOMAINS       
REMARK   3  (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR RATA ANALYSIS AND        
REMARK   3  THEREFORE ARE NOT PRESENT IN THIS STRUCTURE.                        
REMARK   4                                                                      
REMARK   4 2PEA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-07.                  
REMARK 100 THE RCSB ID CODE IS RCSB042281.                                      
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                 : 20MM                               
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : DI-UBIQUITIN, 90% WATER/10%        
REMARK 210                                   D20                                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 15N T1, 15N T2, HETERONUCLEAR      
REMARK 210                                   NOE, HSQC, TOCSY                   
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                 : ELM                                
REMARK 210   METHOD USED                   : NULL                               
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : NULL                               
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 1                                  
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL                
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 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     RES C SSSEQI                                                     
REMARK 465     LEU A    73                                                      
REMARK 465     ARG A    74                                                      
REMARK 465     GLY A    75                                                      
REMARK 465     GLY A    76                                                      
REMARK 465     LEU B    73                                                      
REMARK 465     ARG B    74                                                      
REMARK 465     GLY B    75                                                      
REMARK 465     GLY B    76                                                      
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     8     CG   HIS B    68              1.06            
REMARK 500   O    LEU A     8     ND1  HIS B    68              1.21            
REMARK 500   O    LEU A     8     CD2  HIS B    68              1.73            
REMARK 500   CD1  LEU A     8     CG1  ILE B    44              1.78            
REMARK 500   O    LEU A     8     CE1  HIS B    68              1.88            
REMARK 500   NH1  ARG A    42     NH2  ARG B    42              2.04            
REMARK 500   CA   THR A     9     CE1  HIS B    68              2.14            
REMARK 500   O    LEU A     8     NE2  HIS B    68              2.16            
REMARK 500   O    LEU A     8     CB   HIS B    68              2.17            
REMARK 500   CD1  LEU A     8     CB   ILE B    44              2.18            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500    ARG A  54         0.15    SIDE_CHAIN                              
REMARK 500    ARG A  72         0.25    SIDE_CHAIN                              
REMARK 500    ARG B  54         0.15    SIDE_CHAIN                              
REMARK 500    ARG B  72         0.25    SIDE_CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1D3Z   RELATED DB: PDB                                   
REMARK 900 UBIQUITIN                                                            
REMARK 900 RELATED ID: 1AAR   RELATED DB: PDB                                   
REMARK 900 DI-UBIQUITIN                                                         
REMARK 900 RELATED ID: 2BGF   RELATED DB: PDB                                   
REMARK 900 DI-UBIQUITIN                                                         
REMARK 900 RELATED ID: 2PE9   RELATED DB: PDB                                   
REMARK 900 DI-UBIQUITIN                                                         
DBREF  2PEA A    1    76  UNP    P62988   UBIQ_HUMAN       1     76             
DBREF  2PEA 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  GLY A   35  1                                  14    
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  GLY B   35  1                                  14    
HELIX    5   5 PRO B   37  ASP B   39  5                                   3    
HELIX    6   6 LEU B   56  ASN B   60  5                                   5    
SHEET    1   A 5 THR A  12  GLU A  16  0                                        
SHEET    2   A 5 GLN A   2  LYS A   6 -1  N  VAL A   5   O  ILE A  13           
SHEET    3   A 5 THR A  66  LEU A  71  1  O  LEU A  67   N  PHE A   4           
SHEET    4   A 5 GLN A  41  PHE A  45 -1  N  ILE A  44   O  HIS A  68           
SHEET    5   A 5 LYS A  48  GLN A  49 -1  O  LYS A  48   N  PHE A  45           
SHEET    1   B 5 THR B  12  GLU B  16  0                                        
SHEET    2   B 5 GLN B   2  LYS B   6 -1  N  VAL B   5   O  ILE B  13           
SHEET    3   B 5 THR B  66  LEU B  71  1  O  LEU B  67   N  PHE B   4           
SHEET    4   B 5 GLN B  41  PHE B  45 -1  N  ILE B  44   O  HIS B  68           
SHEET    5   B 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