PDB Short entry for 2BYF
HEADER    LIPASE                                  01-AUG-05   2BYF              
TITLE     NMR SOLUTION STRUCTURE OF PHOSPHOLIPASE C EPSILON RA 2 DOMAIN         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PHOSPHOLIPASE C, EPSILON 1;                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: RA2 DOMAIN, RESIDUES 2131-2246;                            
COMPND   5 SYNONYM: PHOSPHOLIPASE C EPSILON;                                    
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MUTATION: 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 BL21(DE3);                       
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   7 EXPRESSION_SYSTEM_VARIANT: C41;                                      
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PTRIEX4                                   
KEYWDS    PHOSPHOLIPASE C EPSILON, RAS BINDING DOMAIN, UBIQUITIN SUPERFOLD,     
KEYWDS   2 LIPASE                                                               
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    T.D.BUNNEY,R.HARRIS,N.L.GANDARILLAS,M.B.JOSEPHS,S.M.ROE,H.F.PATERSON, 
AUTHOR   2 F.RODRIGUES-LIMA,D.ESPOSITO,P.GIESCHIK,L.H.PEARL,P.C.DRISCOLL,       
AUTHOR   3 M.KATAN                                                              
REVDAT   5   14-JUN-23 2BYF    1       REMARK                                   
REVDAT   4   15-JAN-20 2BYF    1       REMARK                                   
REVDAT   3   24-JAN-18 2BYF    1       SOURCE                                   
REVDAT   2   24-FEB-09 2BYF    1       VERSN                                    
REVDAT   1   22-FEB-06 2BYF    0                                                
JRNL        AUTH   T.D.BUNNEY,R.HARRIS,N.L.GANDARILLAS,M.B.JOSEPHS,S.M.ROE,     
JRNL        AUTH 2 S.C.SORLI,H.F.PATERSON,F.RODRIGUES-LIMA,D.ESPOSITO,          
JRNL        AUTH 3 C.P.PONTING,P.GIERSCHIK,L.H.PEARL,P.C.DRISCOLL,M.KATAN       
JRNL        TITL   STRUCTURAL AND MECHANISTIC INSIGHTS INTO RAS ASSOCIATION     
JRNL        TITL 2 DOMAINS OF PHOSPHOLIPASE C EPSILON.                          
JRNL        REF    MOL.CELL                      V.  21   495 2006              
JRNL        REFN                   ISSN 1097-2765                               
JRNL        PMID   16483931                                                     
JRNL        DOI    10.1016/J.MOLCEL.2006.01.008                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : XPLOR-NIH                                            
REMARK   3   AUTHORS     : C.D. SCHWIETERS, J.J. KUSZEWSKI, N. TJ               
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: AB INITIO SIMULATED ANNEALING PROTOCOL    
REMARK   3  WITH CARTESIAN MOLECULAR DYNAMICS AND TORSION ANGLE DYNAMICS        
REMARK   3  SIMULATED ANNEALING. A FINAL STEP OF RESTRAINED MOLECULAR           
REMARK   3  DYNAMICS WITH EXPLICIT INCLUSION OF SOLVENT.                        
REMARK   4                                                                      
REMARK   4 2BYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-05.                  
REMARK 100 THE DEPOSITION ID IS D_1290025142.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298.0; 298.0                       
REMARK 210  PH                             : 6.5; 6.5                           
REMARK 210  IONIC STRENGTH                 : 275; 275                           
REMARK 210  PRESSURE                       : 1.0 ATM; 1.0 ATM                   
REMARK 210  SAMPLE CONTENTS                : 90% WATER, 10% D2O                 
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : C13-NOESY; N15-NOESY               
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ; 600 MHZ                   
REMARK 210  SPECTROMETER MODEL             : INOVA                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : ANSIG, CNS, XPLOR-NIH              
REMARK 210   METHOD USED                   : RESTRAINED SIMULATED ANNEALING,    
REMARK 210                                   WATER REFINEMENT                   
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : LOWEST ENERGY STRUCTURE WITH NO    
REMARK 210                                   RESTRAINT VIOLATIONS               
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 ON 13C, 15N-LABELED PROTEIN.                           
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 400                                                                      
REMARK 400 COMPOUND                                                             
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 2150 TO LEU                       
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  HD12  LEU A    59     HB3  PHE A   101              1.12            
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   2     -160.48    179.37                                   
REMARK 500  1 GLU A  17       94.20     61.43                                   
REMARK 500  1 GLN A  18       76.52     66.33                                   
REMARK 500  1 TYR A  44      -12.32     70.70                                   
REMARK 500  1 SER A  45      -74.73    -54.72                                   
REMARK 500  1 ASP A  66     -173.84    -60.77                                   
REMARK 500  1 ASN A  69     -152.37    -87.02                                   
REMARK 500  1 CYS A  87      121.52     68.02                                   
REMARK 500  1 GLN A 110       89.82    -50.73                                   
REMARK 500  1 ALA A 111       18.04   -154.27                                   
REMARK 500  1 SER A 112       60.61   -104.81                                   
REMARK 500  1 ARG A 113      -92.53     60.31                                   
REMARK 500  2 SER A  45      -70.43    -64.26                                   
REMARK 500  2 SER A  47       92.13     59.37                                   
REMARK 500  2 LEU A  49       34.63    -84.05                                   
REMARK 500  2 ASP A  66      -97.86    -71.02                                   
REMARK 500  2 THR A  67       88.78   -157.92                                   
REMARK 500  2 ASN A  69      -85.26   -120.79                                   
REMARK 500  2 LYS A  70     -142.70   -128.73                                   
REMARK 500  2 THR A  73     -117.95     51.40                                   
REMARK 500  2 CYS A  87      106.73     68.44                                   
REMARK 500  3 PRO A  16     -144.58    -73.81                                   
REMARK 500  3 GLU A  17      -64.26     71.66                                   
REMARK 500  3 TYR A  44      -43.45     68.42                                   
REMARK 500  3 VAL A  64      105.21    -59.17                                   
REMARK 500  3 ASN A  69      -89.38     54.63                                   
REMARK 500  3 THR A  72       96.71    -67.46                                   
REMARK 500  3 CYS A  87      122.04     73.21                                   
REMARK 500  3 GLU A 114      -71.35     67.14                                   
REMARK 500  4 GLU A   4      114.77    -35.45                                   
REMARK 500  4 PRO A  16     -159.31    -74.50                                   
REMARK 500  4 GLU A  17      -60.51     71.22                                   
REMARK 500  4 TYR A  44      -35.40     74.51                                   
REMARK 500  4 SER A  47       60.95     37.63                                   
REMARK 500  4 LYS A  71      -49.89     72.38                                   
REMARK 500  4 THR A  73       97.83     68.10                                   
REMARK 500  4 CYS A  87      130.49     70.21                                   
REMARK 500  4 GLN A 110       85.40    -56.66                                   
REMARK 500  5 GLU A  17      -56.67     72.93                                   
REMARK 500  5 TYR A  44     -126.66     62.77                                   
REMARK 500  5 SER A  45      -87.57     64.83                                   
REMARK 500  5 SER A  47       78.58     51.46                                   
REMARK 500  5 THR A  68      -85.95     60.07                                   
REMARK 500  5 LEU A  83      -51.68   -131.93                                   
REMARK 500  5 ASP A  84      -38.36    177.34                                   
REMARK 500  5 CYS A  87       96.26     67.84                                   
REMARK 500  5 SER A 112     -168.53   -105.26                                   
REMARK 500  6 ALA A  42       44.99    -81.09                                   
REMARK 500  6 SER A  45      -81.43    -52.80                                   
REMARK 500  6 ASN A  51       68.69     65.66                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     186 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2BYE   RELATED DB: PDB                                   
REMARK 900 NMR SOLUTION STRUCTURE OF PHOSPHOLIPASE C EPSILON RA 1 DOMAIN        
REMARK 900 RELATED ID: 6635   RELATED DB: BMRB                                  
DBREF  2BYF A    1   116  UNP    Q5VWL5   Q5VWL5_HUMAN  2131   2246             
SEQADV 2BYF LEU A   20  UNP  Q5VWL5    ARG  2150 ENGINEERED MUTATION            
SEQRES   1 A  116  SER SER GLU GLU GLU SER PHE PHE VAL GLN VAL HIS ASP          
SEQRES   2 A  116  VAL SER PRO GLU GLN PRO LEU THR VAL ILE LYS ALA PRO          
SEQRES   3 A  116  ARG VAL SER THR ALA GLN ASP VAL ILE GLN GLN THR LEU          
SEQRES   4 A  116  CYS LYS ALA LYS TYR SER TYR SER ILE LEU SER ASN PRO          
SEQRES   5 A  116  ASN PRO SER ASP TYR VAL LEU LEU GLU GLU VAL VAL LYS          
SEQRES   6 A  116  ASP THR THR ASN LYS LYS THR THR THR PRO LYS SER SER          
SEQRES   7 A  116  GLN ARG VAL LEU LEU ASP GLN GLU CYS VAL PHE GLN ALA          
SEQRES   8 A  116  GLN SER LYS TRP LYS GLY ALA GLY LYS PHE ILE LEU LYS          
SEQRES   9 A  116  LEU LYS GLU GLN VAL GLN ALA SER ARG GLU ASP LYS              
HELIX    1   1 THR A   30  ALA A   42  1                                  13    
HELIX    2   2 SER A   47  ASN A   51  5                                   5    
HELIX    3   3 ASN A   53  SER A   55  5                                   3    
HELIX    4   4 CYS A   87  TRP A   95  1                                   9    
SHEET    1  AA 5 LEU A  20  PRO A  26  0                                        
SHEET    2  AA 5 SER A   6  HIS A  12 -1  O  PHE A   7   N  ALA A  25           
SHEET    3  AA 5 LYS A 100  LEU A 105  1  O  PHE A 101   N  HIS A  12           
SHEET    4  AA 5 TYR A  57  VAL A  64 -1  O  VAL A  58   N  LYS A 104           
SHEET    5  AA 5 SER A  77  VAL A  81 -1  O  SER A  78   N  VAL A  63           
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