GenomeNet

Database: PDB
Entry: 3VPV
LinkDB: 3VPV
Original site: 3VPV 
HEADER    TOXIN INHIBITOR                         13-MAR-12   3VPV              
TITLE     CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA TSI2                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TSE2 SPECIFIC IMMUNITY PROTEIN 2;                          
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA;                         
SOURCE   3 ORGANISM_TAXID: 208964;                                              
SOURCE   4 STRAIN: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228;                
SOURCE   5 GENE: PA2703;                                                        
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: B834(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET22B                                    
KEYWDS    TOXIN INHIBITOR                                                       
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    W.WANG,J.DING,D.C.WANG                                                
REVDAT   1   28-MAR-12 3VPV    0                                                
JRNL        AUTH   W.WANG,J.DING,D.C.WANG                                       
JRNL        TITL   CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA TSI2             
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.7_650)                      
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN             
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-                     
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,              
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL            
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE                  
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM             
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,             
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER                
REMARK   3               : ZWART                                                
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.79                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.080                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 96.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 12131                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.186                           
REMARK   3   R VALUE            (WORKING SET) : 0.185                           
REMARK   3   FREE R VALUE                     : 0.216                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.850                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 588                             
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 19.7956 -  2.8553    0.97     2916   154  0.1727 0.1943        
REMARK   3     2  2.8553 -  2.2673    0.96     2897   138  0.1901 0.2354        
REMARK   3     3  2.2673 -  1.9810    0.96     2911   150  0.1835 0.2133        
REMARK   3     4  1.9810 -  1.8000    0.94     2819   146  0.2178 0.2560        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.00                                          
REMARK   3   SHRINKAGE RADIUS   : 0.72                                          
REMARK   3   K_SOL              : 0.41                                          
REMARK   3   B_SOL              : 71.09                                         
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.210            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.310           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 16.88                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 16.23                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -0.44480                                             
REMARK   3    B22 (A**2) : 1.74310                                              
REMARK   3    B33 (A**2) : -1.29830                                             
REMARK   3    B12 (A**2) : 1.31700                                              
REMARK   3    B13 (A**2) : 1.67020                                              
REMARK   3    B23 (A**2) : 1.86560                                              
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.005           1303                                  
REMARK   3   ANGLE     :  0.742           1775                                  
REMARK   3   CHIRALITY :  0.050            197                                  
REMARK   3   PLANARITY :  0.004            244                                  
REMARK   3   DIHEDRAL  : 13.816            491                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 3VPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAR-12.                  
REMARK 100 THE RCSB ID CODE IS RCSB095351.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 14-NOV-11                          
REMARK 200  TEMPERATURE           (KELVIN) : 95                                 
REMARK 200  PH                             : 5.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : BSRF                               
REMARK 200  BEAMLINE                       : 3W1A                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9795                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MAR CCD 165 MM                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 12200                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 19.794                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.4                               
REMARK 200  DATA REDUNDANCY                : 4.000                              
REMARK 200  R MERGE                    (I) : 0.02200                            
REMARK 200  R SYM                      (I) : 0.02200                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 36.5000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.90                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 95.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.00                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.04700                            
REMARK 200  R SYM FOR SHELL            (I) : 0.04700                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 16.000                             
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD                          
REMARK 200 SOFTWARE USED: PHENIX (PHENIX.REFINE: 1.7_650)                       
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 32.27                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.1MM SODIUM ACETATE, PH   
REMARK 280  5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1                              
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 11370 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL                        
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     MSE A     1                                                      
REMARK 465     MSE B     1                                                      
REMARK 465     HIS B    81                                                      
REMARK 465     HIS B    82                                                      
REMARK 465     HIS B    83                                                      
REMARK 465     HIS B    84                                                      
REMARK 465     HIS B    85                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
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    HOH A   196     O    HOH A   213              1.99            
REMARK 500   O    HOH B   156     O    HOH B   162              2.06            
REMARK 500   NE2  GLN A    13     O    HOH A   199              2.06            
REMARK 500   O    HOH A   225     O    HOH B   178              2.09            
REMARK 500   N    ASN B     2     O    HOH B   185              2.09            
REMARK 500   O    HOH A   140     O    HOH A   192              2.10            
REMARK 500   O    HOH B   136     O    HOH B   182              2.15            
REMARK 500   O    HOH A   134     O    HOH A   218              2.17            
REMARK 500   O    HOH A   119     O    HOH A   129              2.17            
REMARK 500   O    HOH A   189     O    HOH A   198              2.17            
REMARK 500   O    HOH A   215     O    HOH A   219              2.18            
REMARK 500   O    HOH B   141     O    HOH B   159              2.18            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
REMARK 500                                                                      
REMARK 500 DISTANCE CUTOFF:                                                     
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
REMARK 500   O    HOH A   218     O    HOH B   172     1655     1.88            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  3VPV A    1    77  UNP    Q9I0D9   Q9I0D9_PSEAE     1     77             
DBREF  3VPV B    1    77  UNP    Q9I0D9   Q9I0D9_PSEAE     1     77             
SEQADV 3VPV LEU A   78  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV GLU A   79  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS A   80  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS A   81  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS A   82  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS A   83  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS A   84  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS A   85  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV LEU B   78  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV GLU B   79  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS B   80  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS B   81  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS B   82  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS B   83  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS B   84  UNP  Q9I0D9              EXPRESSION TAG                 
SEQADV 3VPV HIS B   85  UNP  Q9I0D9              EXPRESSION TAG                 
SEQRES   1 A   85  MSE ASN LEU LYS PRO GLN THR LEU MSE VAL ALA ILE GLN          
SEQRES   2 A   85  CYS VAL ALA ALA ARG THR ARG GLU LEU ASP ALA GLN LEU          
SEQRES   3 A   85  GLN ASN ASP ASP PRO GLN ASN ALA ALA GLU LEU GLU GLN          
SEQRES   4 A   85  LEU LEU VAL GLY TYR ASP LEU ALA ALA ASP ASP LEU LYS          
SEQRES   5 A   85  ASN ALA TYR GLU GLN ALA LEU GLY GLN TYR SER GLY LEU          
SEQRES   6 A   85  PRO PRO TYR ASP ARG LEU ILE GLU GLU PRO ALA SER LEU          
SEQRES   7 A   85  GLU HIS HIS HIS HIS HIS HIS                                  
SEQRES   1 B   85  MSE ASN LEU LYS PRO GLN THR LEU MSE VAL ALA ILE GLN          
SEQRES   2 B   85  CYS VAL ALA ALA ARG THR ARG GLU LEU ASP ALA GLN LEU          
SEQRES   3 B   85  GLN ASN ASP ASP PRO GLN ASN ALA ALA GLU LEU GLU GLN          
SEQRES   4 B   85  LEU LEU VAL GLY TYR ASP LEU ALA ALA ASP ASP LEU LYS          
SEQRES   5 B   85  ASN ALA TYR GLU GLN ALA LEU GLY GLN TYR SER GLY LEU          
SEQRES   6 B   85  PRO PRO TYR ASP ARG LEU ILE GLU GLU PRO ALA SER LEU          
SEQRES   7 B   85  GLU HIS HIS HIS HIS HIS HIS                                  
MODRES 3VPV MSE A    9  MET  SELENOMETHIONINE                                   
MODRES 3VPV MSE B    9  MET  SELENOMETHIONINE                                   
HET    MSE  A   9       8                                                       
HET    MSE  B   9       8                                                       
HETNAM     MSE SELENOMETHIONINE                                                 
FORMUL   1  MSE    2(C5 H11 N O2 SE)                                            
FORMUL   3  HOH   *218(H2 O)                                                    
HELIX    1   1 LYS A    4  GLN A   27  1                                  24    
HELIX    2   2 ASN A   33  ALA A   58  1                                  26    
HELIX    3   3 PRO A   67  ILE A   72  1                                   6    
HELIX    4   4 GLU A   74  GLU A   79  5                                   6    
HELIX    5   5 LYS B    4  ALA B   24  1                                  21    
HELIX    6   6 GLN B   25  ASP B   29  5                                   5    
HELIX    7   7 ASP B   30  GLY B   60  1                                  31    
HELIX    8   8 PRO B   67  GLU B   73  1                                   7    
HELIX    9   9 PRO B   75  GLU B   79  5                                   5    
LINK         C   LEU A   8                 N   MSE A   9     1555   1555  1.33  
LINK         C   MSE A   9                 N   VAL A  10     1555   1555  1.33  
LINK         C   LEU B   8                 N   MSE B   9     1555   1555  1.33  
LINK         C   MSE B   9                 N   VAL B  10     1555   1555  1.33  
CRYST1   28.380   34.920   38.490 110.37  95.98  95.61 P 1           2          
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      0.035236  0.003461  0.005303        0.00000                         
SCALE2      0.000000  0.028775  0.011173        0.00000                         
SCALE3      0.000000  0.000000  0.028023        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
DBGET integrated database retrieval system