GenomeNet

Database: PDB
Entry: 2JQ8
LinkDB: 2JQ8
Original site: 2JQ8 
HEADER    CELL ADHESION                           30-MAY-07   2JQ8              
TITLE     SOLUTION STRUCTURE OF THE SOMATOMEDIN B DOMAIN FROM                   
TITLE    2 VITRONECTIN PRODUCED IN PICHIA PASTORIS                              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: VITRONECTIN;                                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: SEQUENCE DATABASE RESIDUES 20-66;                          
COMPND   5 SYNONYM: SERUM-SPREADING FACTOR, S-PROTEIN, V75;                     
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 GENE: VTN;                                                           
SOURCE   6 EXPRESSION_SYSTEM: PICHIA PASTORIS;                                  
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 4922;                                       
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: X-33;                                      
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE  10 EXPRESSION_SYSTEM_VECTOR: PPICZALPHA A                               
KEYWDS    SOMATOMEDIN B DOMAIN, VITRONECTIN, DISULFIDE-RICH DOMAIN,             
KEYWDS   2 PAI-1, UPAR, CELL ADHESION                                           
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    H.GAARDSVOLL,D.HIRSCHBERG,S.NIELBO,A.MAYASUNDARI,                     
AUTHOR   2 C.B.PETERSON,A.JANSSON,T.J.D.JORGENSEN,F.M.POULSEN                   
REVDAT   2   24-FEB-09 2JQ8    1       VERSN                                    
REVDAT   1   11-SEP-07 2JQ8    0                                                
JRNL        AUTH   M.KJAERGAARD,H.GARDSVOLL,D.HIRSCHBERG,S.NIELBO,              
JRNL        AUTH 2 A.MAYASUNDARI,C.B.PETERSON,A.JANSSON,                        
JRNL        AUTH 3 T.J.D.JORGENSEN,F.M.POULSEN,M.PLOUG                          
JRNL        TITL   SOLUTION STRUCTURE OF RECOMBINANT SOMATOMEDIN B              
JRNL        TITL 2 DOMAIN FROM VITRONECTIN PRODUCED IN PICHIA PASTORIS          
JRNL        REF    PROTEIN SCI.                  V.  16  1934 2007              
JRNL        REFN                   ISSN 0961-8368                               
JRNL        PMID   17766387                                                     
JRNL        DOI    10.1110/PS.072949607                                         
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ         
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2JQ8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-07.                  
REMARK 100 THE RCSB ID CODE IS RCSB100152.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 0                                  
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.4 MM [U-99% 13C; U-99% 15N]      
REMARK 210                                   SMB, 90% H2O/10% D2O; 0.7 MM       
REMARK 210                                   SMB, 90% H2O/10% D2O               
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC, 3D HNCO, 3D        
REMARK 210                                   HNCA, 3D HNCACB, 3D HN(CO)CA,      
REMARK 210                                   3D HN(COCA)CB, 2D 1H-1H NOESY,     
REMARK 210                                   3D 1H-13C NOESY, 3D 1H-15N         
REMARK 210                                   NOESY, 3D HCCH-TOCSY, 3D 1H-       
REMARK 210                                   15N TOCSY                          
REMARK 210  SPECTROMETER FIELD STRENGTH    : 750 MHZ                            
REMARK 210  SPECTROMETER MODEL             : UNITY                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : PRONTO, NMRDRAW, SPARKY, CYANA     
REMARK 210   METHOD USED                   : MOLECULAR 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 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 1-20                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     HIS A    48                                                      
REMARK 465     HIS A    49                                                      
REMARK 465     HIS A    50                                                      
REMARK 465     HIS A    51                                                      
REMARK 465     HIS A    52                                                      
REMARK 465     HIS A    53                                                      
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 LYS A   6      -99.02   -129.93                                   
REMARK 500  1 ARG A   8       45.54    -85.94                                   
REMARK 500  1 LYS A  40       76.16     61.52                                   
REMARK 500  1 GLN A  42       71.19     64.46                                   
REMARK 500  1 THR A  44      -77.21    -56.68                                   
REMARK 500  2 LYS A   6      -88.32   -151.51                                   
REMARK 500  2 PHE A  13      109.12    -56.94                                   
REMARK 500  2 VAL A  15       39.08    -78.83                                   
REMARK 500  2 ASP A  16       29.19   -151.35                                   
REMARK 500  2 LYS A  18      -74.09    -64.13                                   
REMARK 500  2 ARG A  45      -71.69    -74.26                                   
REMARK 500  3 GLN A   2       18.04   -158.85                                   
REMARK 500  3 LYS A   6     -104.42   -144.48                                   
REMARK 500  3 ASP A  16      -30.66   -151.67                                   
REMARK 500  3 ASP A  34       40.22    -92.14                                   
REMARK 500  3 GLN A  42       79.49     64.44                                   
REMARK 500  4 GLN A   2       23.68   -148.01                                   
REMARK 500  4 GLU A   3       47.52    -97.09                                   
REMARK 500  4 LYS A   6      -68.63   -123.13                                   
REMARK 500  4 CYS A   9       45.25   -166.92                                   
REMARK 500  4 THR A  10      -37.26   -163.86                                   
REMARK 500  4 SER A  30       48.42   -148.77                                   
REMARK 500  5 GLN A   2      -31.23    170.74                                   
REMARK 500  5 GLU A   3       41.53   -100.07                                   
REMARK 500  5 LYS A   6      -52.10   -125.90                                   
REMARK 500  5 VAL A  15       41.13    -78.54                                   
REMARK 500  5 ASP A  16       24.32   -166.69                                   
REMARK 500  5 LYS A  17     -103.44    -89.30                                   
REMARK 500  5 LYS A  18      -56.06   -150.48                                   
REMARK 500  5 LYS A  40       78.00     59.32                                   
REMARK 500  5 THR A  44     -157.57    -80.43                                   
REMARK 500  6 LYS A   6      -89.83   -128.34                                   
REMARK 500  6 VAL A  15       41.28    -78.80                                   
REMARK 500  6 LYS A  40       79.81     60.64                                   
REMARK 500  6 ARG A  45      -59.32     71.97                                   
REMARK 500  7 GLN A   2       53.06   -151.46                                   
REMARK 500  7 LYS A   6      -79.42   -134.58                                   
REMARK 500  7 VAL A  15       36.03    -86.11                                   
REMARK 500  7 SER A  30       76.64   -154.34                                   
REMARK 500  7 LYS A  40       75.54     52.04                                   
REMARK 500  7 PRO A  41       38.39    -79.17                                   
REMARK 500  7 GLN A  42      -44.06     79.56                                   
REMARK 500  7 VAL A  43      121.42     77.65                                   
REMARK 500  7 ARG A  45       58.78    -91.92                                   
REMARK 500  8 LYS A   6      -88.08    -98.71                                   
REMARK 500  8 ASP A  16       41.04    -94.54                                   
REMARK 500  8 LYS A  40       75.56     57.72                                   
REMARK 500  8 GLN A  42      -12.01     71.53                                   
REMARK 500  9 GLN A   2       21.04   -155.46                                   
REMARK 500  9 LYS A   6      -81.79   -134.28                                   
REMARK 500  9 CYS A   9       18.64   -150.64                                   
REMARK 500  9 THR A  10      -36.65   -147.69                                   
REMARK 500  9 ASP A  16      -41.99   -157.52                                   
REMARK 500  9 SER A  30       54.34   -140.22                                   
REMARK 500  9 LYS A  40       78.19     61.28                                   
REMARK 500  9 GLN A  42      142.42     72.50                                   
REMARK 500  9 THR A  44       63.45     60.07                                   
REMARK 500 10 GLU A   3      129.67     80.42                                   
REMARK 500 10 LYS A   6       31.08   -151.71                                   
REMARK 500 10 CYS A   9        1.74    -68.70                                   
REMARK 500 10 ASP A  16      -41.35   -155.01                                   
REMARK 500 10 ASP A  34       31.29    -91.00                                   
REMARK 500 10 LYS A  40       74.87     60.24                                   
REMARK 500 10 GLN A  42      139.84   -172.73                                   
REMARK 500 10 THR A  44     -161.32   -119.52                                   
REMARK 500 11 LYS A   6      -33.77   -164.01                                   
REMARK 500 11 VAL A  15       42.67    -78.53                                   
REMARK 500 11 LYS A  18      -61.88    -93.46                                   
REMARK 500 11 LYS A  40       77.50     59.36                                   
REMARK 500 12 ARG A   8       40.85    -98.62                                   
REMARK 500 12 VAL A  15       41.32    -80.78                                   
REMARK 500 12 SER A  30       56.74   -141.77                                   
REMARK 500 12 LYS A  40       85.10     58.07                                   
REMARK 500 12 GLN A  42       86.69     61.81                                   
REMARK 500 13 LYS A   6      -64.26   -162.48                                   
REMARK 500 13 VAL A  15       35.97    -78.47                                   
REMARK 500 13 LYS A  17     -169.52   -109.08                                   
REMARK 500 13 LYS A  18      -63.79    -96.17                                   
REMARK 500 13 ASP A  34       32.88    -92.43                                   
REMARK 500 13 THR A  44       38.98    -75.90                                   
REMARK 500 14 LYS A   6       28.91   -146.58                                   
REMARK 500 14 PHE A  13      107.36    -56.22                                   
REMARK 500 14 SER A  30       48.24   -142.04                                   
REMARK 500 14 GLN A  42      -69.60   -160.40                                   
REMARK 500 14 ARG A  45       48.05   -101.36                                   
REMARK 500 15 LYS A   6      -60.98   -141.63                                   
REMARK 500 15 SER A  30       76.47   -151.39                                   
REMARK 500 15 LYS A  40      102.85     64.95                                   
REMARK 500 16 LYS A   6      -78.02   -118.82                                   
REMARK 500 16 SER A  30       46.73   -141.94                                   
REMARK 500 16 LYS A  40       75.40     55.30                                   
REMARK 500 16 ARG A  45      -98.92   -123.58                                   
REMARK 500 17 GLU A   3     -158.54    -94.42                                   
REMARK 500 17 LYS A  40       92.05     60.76                                   
REMARK 500 17 PRO A  41     -149.05    -81.10                                   
REMARK 500 17 VAL A  43      101.39     66.93                                   
REMARK 500 17 THR A  44       83.77    -68.76                                   
REMARK 500 18 GLN A   2       83.07     59.37                                   
REMARK 500 18 GLU A   3       97.23    -69.71                                   
REMARK 500 18 SER A   4      107.38   -168.38                                   
REMARK 500 18 LYS A   6     -101.30   -147.48                                   
REMARK 500 18 CYS A   9       10.87   -148.11                                   
REMARK 500 18 SER A  30       77.21   -150.68                                   
REMARK 500 18 ASP A  34       32.97    -94.38                                   
REMARK 500 18 LYS A  40       66.59     63.19                                   
REMARK 500 18 THR A  44      104.81    -55.97                                   
REMARK 500 19 LYS A   6      -70.70   -122.66                                   
REMARK 500 19 LYS A  40       73.09     55.94                                   
REMARK 500 20 GLU A   3     -111.44    -78.91                                   
REMARK 500 20 LYS A   6      -36.51    176.96                                   
REMARK 500 20 VAL A  15       47.03    -78.32                                   
REMARK 500 20 ASP A  16      -35.42   -138.09                                   
REMARK 500 20 LYS A  40       84.60     62.46                                   
REMARK 500 20 GLN A  42      105.29    -18.13                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1SSU   RELATED DB: PDB                                   
REMARK 900 SAME DOMAIN, WRONG DISULFIDES                                        
REMARK 900 RELATED ID: 1S4G   RELATED DB: PDB                                   
REMARK 900 SAME DOMAIN, WRONG DISULFIDES                                        
REMARK 900 RELATED ID: 1OC0   RELATED DB: PDB                                   
REMARK 900 COMPLEX OF SAME DOMAIN                                               
REMARK 900 RELATED ID: 6160   RELATED DB: BMRB                                  
REMARK 900 SAME DOMAIN, HOMONUCLEAR                                             
REMARK 900 RELATED ID: 15271   RELATED DB: BMRB                                 
DBREF  2JQ8 A    1    47  UNP    P04004   VTNC_HUMAN      20     66             
SEQADV 2JQ8 HIS A   48  UNP  P04004              EXPRESSION TAG                 
SEQADV 2JQ8 HIS A   49  UNP  P04004              EXPRESSION TAG                 
SEQADV 2JQ8 HIS A   50  UNP  P04004              EXPRESSION TAG                 
SEQADV 2JQ8 HIS A   51  UNP  P04004              EXPRESSION TAG                 
SEQADV 2JQ8 HIS A   52  UNP  P04004              EXPRESSION TAG                 
SEQADV 2JQ8 HIS A   53  UNP  P04004              EXPRESSION TAG                 
SEQRES   1 A   53  ASP GLN GLU SER CYS LYS GLY ARG CYS THR GLU GLY PHE          
SEQRES   2 A   53  ASN VAL ASP LYS LYS CYS GLN CYS ASP GLU LEU CYS SER          
SEQRES   3 A   53  TYR TYR GLN SER CYS CYS THR ASP TYR THR ALA GLU CYS          
SEQRES   4 A   53  LYS PRO GLN VAL THR ARG GLY ASP HIS HIS HIS HIS HIS          
SEQRES   5 A   53  HIS                                                          
HELIX    1   1 LEU A   24  GLN A   29  1                                   6    
HELIX    2   2 ASP A   34  CYS A   39  1                                   6    
SSBOND   1 CYS A    5    CYS A   21                          1555   1555  2.02  
SSBOND   2 CYS A    9    CYS A   39                          1555   1555  2.03  
SSBOND   3 CYS A   19    CYS A   32                          1555   1555  2.02  
SSBOND   4 CYS A   25    CYS A   31                          1555   1555  2.03  
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                                                                             
DBGET integrated database retrieval system