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Database: PDB
Entry: 1SSU
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Original site: 1SSU 
HEADER    CELL ADHESION                           24-MAR-04   1SSU              
TITLE     STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR DISULFIDE BOND                
TITLE    2 HETEROGENEITY IN ACTIVE FORMS OF THE SOMATOMEDIN B DOMAIN            
TITLE    3 OF HUMAN VITRONECTIN                                                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: VITRONECTIN;                                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: SOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN;                 
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 GENE: VTN;                                                           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21TRXB(DE3);                             
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET-32A                                   
KEYWDS    SOMATOSTATIN B DOMAIN, VITRONECTIN, NMR STRUCTURE,                    
KEYWDS   2 DISULFIDE BONDS HETEROGENEITY, CELL ADHESION                         
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    Y.KAMIKUBO,R.DE GUZMAN,G.KROON,S.CURRIDEN,J.G.NEELS,                  
AUTHOR   2 M.J.CHURCHILL,P.DAWSON,S.OLDZIEJ,A.JAGIELSKA,H.A.SCHERAGA,           
AUTHOR   3 D.J.LOSKUTOFF,H.J.DYSON                                              
REVDAT   2   24-FEB-09 1SSU    1       VERSN                                    
REVDAT   1   27-JUL-04 1SSU    0                                                
JRNL        AUTH   Y.KAMIKUBO,R.DE GUZMAN,G.KROON,S.CURRIDEN,                   
JRNL        AUTH 2 J.G.NEELS,M.J.CHURCHILL,P.DAWSON,S.OLDZIEJ,                  
JRNL        AUTH 3 A.JAGIELSKA,H.A.SCHERAGA,D.J.LOSKUTOFF,H.J.DYSON             
JRNL        TITL   DISULFIDE BONDING ARRANGEMENTS IN ACTIVE FORMS OF            
JRNL        TITL 2 THE SOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN.               
JRNL        REF    BIOCHEMISTRY                  V.  43  6519 2004              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   15157085                                                     
JRNL        DOI    10.1021/BI049647C                                            
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : AMBER 7                                              
REMARK   3   AUTHORS     : D. CASE, D. PEARLMAN ET AL.                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1SSU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-04.                  
REMARK 100 THE RCSB ID CODE IS RCSB021972.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 293; 293                           
REMARK 210  PH                             : 7.5; 7.5                           
REMARK 210  IONIC STRENGTH                 : 180 MM; 180 MM                     
REMARK 210  PRESSURE                       : 1 ATM; 1 ATM                       
REMARK 210  SAMPLE CONTENTS                : N15-LABELED PROTEIN 20 MM          
REMARK 210                                   SODIUM PHOSPHATE PH 7.5;           
REMARK 210                                   UNLABELED PROTEIN 20 MM SODIUM     
REMARK 210                                   PHOSPHATE PH 7.5                   
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D NOESY, 2D TOCSY, 3D_15N-        
REMARK 210                                   SEPARATED_NOESY                    
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ, 750 MHZ, 900 MHZ          
REMARK 210  SPECTROMETER MODEL             : AVANCE, DRX                        
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : DYANA 1.5, AMBER 7, NMRPIPE        
REMARK 210                                   2003, NMRVIEW 4.1.3                
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS IN          
REMARK 210                                   DYANA FOLLOWED BY SIMULATED        
REMARK 210                                   ANNEALING AND ENERGY               
REMARK 210                                   MINIMIZATION IN AMBER              
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 200                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : 20 LOWEST ENERGY STRUCTURES        
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NOT APPLICABLE                                               
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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500  1 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES          
REMARK 500  3 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   3.8 DEGREES          
REMARK 500  6 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES          
REMARK 500  7 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 DEGREES          
REMARK 500 10 CYS A  21   CA  -  CB  -  SG  ANGL. DEV. =   6.7 DEGREES          
REMARK 500 10 ARG A  45   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES          
REMARK 500 11 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   4.1 DEGREES          
REMARK 500 12 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES          
REMARK 500 13 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 DEGREES          
REMARK 500 14 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 DEGREES          
REMARK 500 15 ARG A  45   NE  -  CZ  -  NH1 ANGL. DEV. =   3.8 DEGREES          
REMARK 500 16 CYS A   5   CA  -  CB  -  SG  ANGL. DEV. =   9.0 DEGREES          
REMARK 500 17 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 DEGREES          
REMARK 500 18 CYS A   5   CA  -  CB  -  SG  ANGL. DEV. =   8.6 DEGREES          
REMARK 500 18 CYS A  21   CA  -  CB  -  SG  ANGL. DEV. =   8.1 DEGREES          
REMARK 500 20 ARG A   8   NE  -  CZ  -  NH1 ANGL. DEV. =   3.8 DEGREES          
REMARK 500 20 CYS A  39   CA  -  CB  -  SG  ANGL. DEV. =   8.1 DEGREES          
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  14       89.41   -160.53                                   
REMARK 500  1 CYS A  21       48.15    -75.84                                   
REMARK 500  1 ASP A  34       38.65   -143.43                                   
REMARK 500  1 PRO A  41      158.83    -46.13                                   
REMARK 500  1 PHE A  49       30.82   -146.26                                   
REMARK 500  2 ASN A  14       98.17   -167.87                                   
REMARK 500  2 CYS A  32      155.71    -48.33                                   
REMARK 500  2 LYS A  40      109.21    -40.25                                   
REMARK 500  2 PHE A  49      -43.75   -164.87                                   
REMARK 500  2 THR A  50       21.10   -140.23                                   
REMARK 500  3 LYS A   6       90.57    -69.71                                   
REMARK 500  3 ARG A   8      -30.53   -134.11                                   
REMARK 500  3 ASN A  14       84.65   -161.01                                   
REMARK 500  3 CYS A  21       46.88    -74.43                                   
REMARK 500  3 ASP A  34       38.45   -141.44                                   
REMARK 500  4 ASN A  14      114.08   -163.42                                   
REMARK 500  4 GLN A  20       64.84   -109.20                                   
REMARK 500  4 CYS A  21       42.36    -69.30                                   
REMARK 500  5 LYS A   6       91.07    -69.74                                   
REMARK 500  5 ARG A   8      -35.04   -132.10                                   
REMARK 500  5 ASN A  14       89.87   -164.70                                   
REMARK 500  5 VAL A  15       -8.21    -58.89                                   
REMARK 500  5 GLN A  20       66.88   -102.45                                   
REMARK 500  5 CYS A  21       47.90    -72.67                                   
REMARK 500  5 ASP A  34       32.56   -140.50                                   
REMARK 500  5 TYR A  35      -56.11    -29.82                                   
REMARK 500  5 LYS A  40      105.38    -38.51                                   
REMARK 500  5 PRO A  41     -169.46    -79.05                                   
REMARK 500  5 GLN A  42      150.90    -49.90                                   
REMARK 500  6 CYS A   9      124.61    -38.16                                   
REMARK 500  6 GLN A  20       65.01   -100.31                                   
REMARK 500  6 CYS A  21       38.43    -67.15                                   
REMARK 500  6 ASP A  47       28.70   -141.92                                   
REMARK 500  7 CYS A  21       38.48    -73.32                                   
REMARK 500  7 LYS A  40      101.51    -37.27                                   
REMARK 500  7 PRO A  41       16.31    -62.50                                   
REMARK 500  8 LYS A   6       79.96    -69.47                                   
REMARK 500  8 ASN A  14      103.16   -160.73                                   
REMARK 500  8 CYS A  21       33.48    -65.91                                   
REMARK 500  8 ASP A  34       40.77   -144.13                                   
REMARK 500  8 PRO A  41     -176.62    -57.14                                   
REMARK 500  9 LYS A   6       97.33    -69.69                                   
REMARK 500  9 CYS A   9       15.48    -53.91                                   
REMARK 500  9 THR A  10       15.60   -142.28                                   
REMARK 500  9 GLN A  20       65.02   -111.36                                   
REMARK 500  9 VAL A  43       39.38    -74.14                                   
REMARK 500 10 LYS A   6       89.13    -69.86                                   
REMARK 500 10 CYS A  21       36.66    -72.11                                   
REMARK 500 10 CYS A  32      147.26    -39.83                                   
REMARK 500 10 LYS A  40      106.87    -40.93                                   
REMARK 500 10 THR A  44       31.60   -148.42                                   
REMARK 500 10 VAL A  48       32.38    -75.07                                   
REMARK 500 10 PHE A  49      -28.80   -150.03                                   
REMARK 500 10 THR A  50       27.28    -79.73                                   
REMARK 500 11 GLU A   3       82.96   -151.08                                   
REMARK 500 11 LYS A   6       95.61    -69.44                                   
REMARK 500 11 GLN A  20       63.53   -106.53                                   
REMARK 500 11 CYS A  21       43.87    -68.56                                   
REMARK 500 11 LYS A  40       89.49    -22.05                                   
REMARK 500 12 LYS A   6       98.04    -69.16                                   
REMARK 500 12 GLN A  20       58.06   -105.31                                   
REMARK 500 12 CYS A  21       41.23    -67.03                                   
REMARK 500 12 ASP A  47       22.61   -143.99                                   
REMARK 500 13 ARG A   8      -36.16   -134.97                                   
REMARK 500 13 GLN A  20       64.96   -106.71                                   
REMARK 500 13 CYS A  21       49.49    -71.21                                   
REMARK 500 13 GLU A  38      -51.41   -120.53                                   
REMARK 500 13 LYS A  40       98.91    -35.64                                   
REMARK 500 13 PRO A  41     -168.62    -79.29                                   
REMARK 500 14 LYS A   6       93.98    -69.08                                   
REMARK 500 14 CYS A  21       42.07    -70.31                                   
REMARK 500 14 CYS A  31      175.30    -57.24                                   
REMARK 500 14 ASP A  34       41.12   -143.47                                   
REMARK 500 14 LYS A  40       99.45    -37.47                                   
REMARK 500 14 GLN A  42       49.25     23.43                                   
REMARK 500 15 LYS A   6       98.46    -69.24                                   
REMARK 500 15 CYS A   9        4.77    -49.66                                   
REMARK 500 15 THR A  10       20.61   -142.38                                   
REMARK 500 15 ASN A  14      100.13   -162.50                                   
REMARK 500 15 GLN A  20       55.33   -111.30                                   
REMARK 500 15 CYS A  21       53.07    -69.09                                   
REMARK 500 15 GLN A  42       49.83    -77.85                                   
REMARK 500 15 THR A  44       41.19   -150.43                                   
REMARK 500 16 LYS A   6       97.93    -69.03                                   
REMARK 500 16 ARG A   8      -34.75   -144.73                                   
REMARK 500 16 ASN A  14      101.60   -166.65                                   
REMARK 500 16 CYS A  21       47.91    -72.54                                   
REMARK 500 16 GLU A  38      -62.96   -120.62                                   
REMARK 500 16 LYS A  40      108.95    -39.17                                   
REMARK 500 17 ARG A   8      -38.18   -133.06                                   
REMARK 500 17 CYS A   9      142.96    -38.70                                   
REMARK 500 17 THR A  10       38.20     70.94                                   
REMARK 500 17 ASN A  14       81.06   -154.34                                   
REMARK 500 17 CYS A  32      154.54    -48.68                                   
REMARK 500 17 ASP A  34       36.33   -141.71                                   
REMARK 500 17 LYS A  40       91.72    -21.43                                   
REMARK 500 17 PRO A  41     -167.07    -78.87                                   
REMARK 500 17 PHE A  49       19.16   -141.22                                   
REMARK 500 18 LYS A   6      100.00    -68.49                                   
REMARK 500 18 ARG A   8      -28.68   -141.40                                   
REMARK 500 18 GLN A  20       69.93   -115.22                                   
REMARK 500 18 CYS A  21       38.46    -70.31                                   
REMARK 500 18 CYS A  32      156.28    -39.90                                   
REMARK 500 18 GLU A  38      -72.01   -120.64                                   
REMARK 500 18 LYS A  40       95.37    -29.87                                   
REMARK 500 18 PRO A  41       44.19    -76.86                                   
REMARK 500 18 GLN A  42       35.26   -140.84                                   
REMARK 500 18 THR A  44       28.89   -140.45                                   
REMARK 500 19 ASN A  14       90.66   -161.16                                   
REMARK 500 19 CYS A  21       47.04    -81.10                                   
REMARK 500 19 PRO A  41      165.67    -48.81                                   
REMARK 500 19 GLN A  42       87.45    -64.06                                   
REMARK 500 19 ASP A  47       28.59    -69.45                                   
REMARK 500 20 ARG A   8      -30.31   -134.73                                   
REMARK 500 20 ASN A  14      101.95   -162.24                                   
REMARK 500 20 CYS A  21       43.47    -77.68                                   
REMARK 500 20 CYS A  32      152.30    -47.11                                   
REMARK 500 20 LYS A  40      108.51    -46.78                                   
REMARK 500 20 GLN A  42       66.54     26.08                                   
REMARK 500 20 PHE A  49      -28.92   -157.28                                   
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 11 TYR A  35         0.07    SIDE_CHAIN                              
REMARK 500 16 TYR A  35         0.08    SIDE_CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1SSU A    1    51  UNP    P04004   VTNC_HUMAN      20     70             
SEQRES   1 A   51  ASP GLN GLU SER CYS LYS GLY ARG CYS THR GLU GLY PHE          
SEQRES   2 A   51  ASN VAL ASP LYS LYS CYS GLN CYS ASP GLU LEU CYS SER          
SEQRES   3 A   51  TYR TYR GLN SER CYS CYS THR ASP TYR THR ALA GLU CYS          
SEQRES   4 A   51  LYS PRO GLN VAL THR ARG GLY ASP VAL PHE THR MET              
HELIX    1   1 LEU A   24  TYR A   28  5                                   5    
HELIX    2   2 ASP A   34  CYS A   39  1                                   6    
SSBOND   1 CYS A    5    CYS A    9                          1555   1555  2.04  
SSBOND   2 CYS A   19    CYS A   21                          1555   1555  2.06  
SSBOND   3 CYS A   25    CYS A   31                          1555   1555  2.02  
SSBOND   4 CYS A   32    CYS A   39                          1555   1555  2.04  
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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