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Promode Elastic




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    HEADER    IMMUNE SYSTEM, PROTEIN BINDING          28-MAR-06   2GI9              
    TITLE     BACKBONE CONFORMATIONAL CONSTRAINTS IN A MICROCRYSTALLINE U-          
    TITLE    2 15N-LABELED PROTEIN BY 3D DIPOLAR-SHIFT SOLID-STATE NMR              
    TITLE    3 SPECTROSCOPY                                                         
    COMPND    MOL_ID: 1;                                                            
    COMPND   2 MOLECULE: IMMUNOGLOBULIN B1 BINDING DOMAIN OF PROTEIN G;             
    COMPND   3 CHAIN: A;                                                            
    COMPND   4 SYNONYM: IGG BINDING PROTEIN G;                                      
    COMPND   5 ENGINEERED: YES;                                                     
    COMPND   6 MUTATION: YES                                                        
    SOURCE    MOL_ID: 1;                                                            
    SOURCE   2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS;                          
    SOURCE   3 ORGANISM_TAXID: 1280;                                                
    SOURCE   4 GENE: SPG;                                                           
    SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
    SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562                                         
    KEYWDS    GB1, IMMUNE SYSTEM, PROTEIN BINDING                                   
    EXPDTA    X-RAY DIFFRACTION                                                     
    AUTHOR    W.T.FRANKS,B.J.WYLIE,S.A.STELLFOX,C.M.RIENSTRA                        
    REVDAT   4   29-DEC-09 2GI9    1       EXPDTA REMARK                            
    REVDAT   3   24-FEB-09 2GI9    1       VERSN                                    
    REVDAT   2   06-JUN-06 2GI9    1       COMPND HEADER                            
    REVDAT   1   25-APR-06 2GI9    0                                                
    JRNL        AUTH   W.T.FRANKS,B.J.WYLIE,S.A.STELLFOX,C.M.RIENSTRA               
    JRNL        TITL   BACKBONE CONFORMATIONAL CONSTRAINTS IN A                     
    JRNL        TITL 2 MICROCRYSTALLINE U-15N-LABELED PROTEIN BY 3D                 
    JRNL        TITL 3 DIPOLAR-SHIFT SOLID-STATE NMR SPECTROSCOPY                   
    JRNL        REF    J.AM.CHEM.SOC.                V. 128  3154 2006              
    JRNL        REFN                   ISSN 0002-7863                               
    JRNL        PMID   16522090                                                     
    JRNL        DOI    10.1021/JA058292X                                            
    REMARK   1                                                                      
    REMARK   2                                                                      
    REMARK   2 RESOLUTION.    1.14 ANGSTROMS.                                       
    REMARK   3                                                                      
    REMARK   3 REFINEMENT.                                                          
    REMARK   3   PROGRAM     : SHELXL-97                                            
    REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
    REMARK   3                                                                      
    REMARK   3  DATA USED IN REFINEMENT.                                            
    REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14                           
    REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 50.00                          
    REMARK   3   DATA CUTOFF            (SIGMA(F)) : 4.000                          
    REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.6                           
    REMARK   3   CROSS-VALIDATION METHOD           : FREE R                         
    REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM                         
    REMARK   3                                                                      
    REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
    REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.193                  
    REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.167                  
    REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.181                  
    REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.000                  
    REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 787                    
    REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 16502                  
    REMARK   3                                                                      
    REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
    REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.190                  
    REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL                   
    REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL                   
    REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000                  
    REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
    REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 15760                  
    REMARK   3                                                                      
    REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
    REMARK   3   PROTEIN ATOMS      : 438                                           
    REMARK   3   NUCLEIC ACID ATOMS : 0                                             
    REMARK   3   HETEROGEN ATOMS    : 0                                             
    REMARK   3   SOLVENT ATOMS      : 119                                           
    REMARK   3                                                                      
    REMARK   3  MODEL REFINEMENT.                                                   
    REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 557.00                  
    REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00                    
    REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 0                       
    REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 3                       
    REMARK   3   NUMBER OF RESTRAINTS                     : 1803                    
    REMARK   3                                                                      
    REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
    REMARK   3   BOND LENGTHS                         (A) : 0.013                   
    REMARK   3   ANGLE DISTANCES                      (A) : 0.030                   
    REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000                   
    REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.031                   
    REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.063                   
    REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.084                   
    REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.015                   
    REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.000                   
    REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.075                   
    REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : 0.000                   
    REMARK   3                                                                      
    REMARK   3  BULK SOLVENT MODELING.                                              
    REMARK   3   METHOD USED: NULL                                                  
    REMARK   3                                                                      
    REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER                      
    REMARK   3   SPECIAL CASE: NULL                                                 
    REMARK   3                                                                      
    REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
    REMARK   4                                                                      
    REMARK   4 2GI9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
    REMARK 100                                                                      
    REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-06.                  
    REMARK 100 THE RCSB ID CODE IS RCSB037151.                                      
    REMARK 200                                                                      
    REMARK 200 EXPERIMENTAL DETAILS                                                 
    REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
    REMARK 200  DATE OF DATA COLLECTION        : 01-NOV-05                          
    REMARK 200  TEMPERATURE           (KELVIN) : NULL                               
    REMARK 200  PH                             : 4.50                               
    REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
    REMARK 200                                                                      
    REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
    REMARK 200  RADIATION SOURCE               : NSLS                               
    REMARK 200  BEAMLINE                       : X12C                               
    REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
    REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
    REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9791                             
    REMARK 200  MONOCHROMATOR                  : NULL                               
    REMARK 200  OPTICS                         : NULL                               
    REMARK 200                                                                      
    REMARK 200  DETECTOR TYPE                  : CCD                                
    REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 210                   
    REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
    REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
    REMARK 200                                                                      
    REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 16662                              
    REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.140                              
    REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
    REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
    REMARK 200                                                                      
    REMARK 200 OVERALL.                                                             
    REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.3                               
    REMARK 200  DATA REDUNDANCY                : NULL                               
    REMARK 200  R MERGE                    (I) : NULL                               
    REMARK 200  R SYM                      (I) : NULL                               
    REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
    REMARK 200                                                                      
    REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
    REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
    REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
    REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
    REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
    REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
    REMARK 200  R SYM FOR SHELL            (I) : NULL                               
    REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
    REMARK 200                                                                      
    REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
    REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO                    
    REMARK 200 SOFTWARE USED: SHELX                                                 
    REMARK 200 STARTING MODEL: NULL                                                 
    REMARK 200                                                                      
    REMARK 200 REMARK: NULL                                                         
    REMARK 280                                                                      
    REMARK 280 CRYSTAL                                                              
    REMARK 280 SOLVENT CONTENT, VS   (%): 36.00                                     
    REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92                     
    REMARK 280                                                                      
    REMARK 280 CRYSTALLIZATION CONDITIONS: 5MM ACETATE 3.8, 150MM NACL, 50%         
    REMARK 280  MPD AND 20% IPA, PH 4.5                                             
    REMARK 290                                                                      
    REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
    REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
    REMARK 290                                                                      
    REMARK 290      SYMOP   SYMMETRY                                                
    REMARK 290     NNNMMM   OPERATOR                                                
    REMARK 290       1555   X,Y,Z                                                   
    REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
    REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
    REMARK 290       4555   X+1/2,-Y+1/2,-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   SMTRY1   2 -1.000000  0.000000  0.000000       12.59850            
    REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
    REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       25.13700            
    REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
    REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       18.19200            
    REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       25.13700            
    REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       12.59850            
    REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       18.19200            
    REMARK 290   SMTRY3   4  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: 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 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    LEU A  12   CB  -  CG  -  CD2 ANGL. DEV. =  20.2 DEGREES          
    REMARK 500    TYR A  45   CB  -  CG  -  CD1 ANGL. DEV. =  -4.3 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    ASN A   8       65.49   -119.89                                   
    REMARK 500                                                                      
    REMARK 500 REMARK: NULL                                                         
    REMARK 900                                                                      
    REMARK 900 RELATED ENTRIES                                                      
    REMARK 900 RELATED ID: 1PGA   RELATED DB: PDB                                   
    REMARK 900 ALTERNATE CRYSTAL STRUCTURE                                          
    DBREF  2GI9 A    1    56  UNP    P19909   SPG2_STRSG     303    357             
    SEQADV 2GI9 MET A    1  UNP  P19909              INITIATING METHIONINE          
    SEQADV 2GI9 GLN A    2  UNP  P19909    THR   303 ENGINEERED                     
    SEQRES   1 A   56  MET GLN TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS          
    SEQRES   2 A   56  GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA          
    SEQRES   3 A   56  GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL          
    SEQRES   4 A   56  ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE          
    SEQRES   5 A   56  THR VAL THR GLU                                              
    FORMUL   2  HOH   *119(H2 O)                                                    
    HELIX    1   1 ASP A   22  ASN A   37  1                                  16    
    SHEET    1   A 4 LYS A  13  GLU A  19  0                                        
    SHEET    2   A 4 GLN A   2  ASN A   8 -1  N  LEU A   7   O  GLY A  14           
    SHEET    3   A 4 THR A  51  THR A  55  1  O  PHE A  52   N  LYS A   4           
    SHEET    4   A 4 GLU A  42  ASP A  46 -1  N  GLU A  42   O  THR A  55           
    CRYST1   25.197   36.384   50.274  90.00  90.00  90.00 P 21 21 21    4          
    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      0.039687  0.000000  0.000000        0.00000                         
    SCALE2      0.000000  0.027485  0.000000        0.00000                         
    SCALE3      0.000000  0.000000  0.019891        0.00000                         

    3D molecular view of vibration

    Displacement vectors
    Display
    Animation
    Display

    Still image of displacement vectors and GIF animation


    Mode 1

    Time-average properties and properties of the 10 lowest-frequency modes

    Fluctuation of atoms:
    Time average and for the 3 lowest-frequency modes.
    Fluctuation of dihedral angles:
    Time average and for the 3 lowest-frequency modes.
    Fluctuation of atomsFluctuation of dihedral angles

    Correlations between fluctuations of atoms

    Mode 1
    Correlations between fluctuations of atoms - Mode 1
    Time Average
    Time Average
    Distance map
    Distance map

    Calculation note

    PDB file name : pdb2gi9.ent

    Chains and HETATMs selected: 
      ATOM        A

    = Normal mode analysis calculation =

    No. of modes used in the calculation : All modes.

    Parameters of potential energies:
      1-4 and 1-5 non-bonded interactions: E(d) = A*exp(-d(PDB)**2/B**2)(d-d(PDB))**2.
      Loop-closing potential:              E(d) = A*(d-d(PDB))**2.
        for a disulfide bond and one of the bonds in the DNA and RNA sugar ring.
      where d and d(PDB) are distances between atoms in calculation and in PDB data, 
      respectively.

      Interaction type   A       B      Cutoff distance (A)
        1-4             1.00    5.00      100.00
        1-5             1.00    5.00      100.00
        Loop-closing  100.00

    Temperature adjustment by magnitude of fluctuation:
      Set to mean displacements of atoms       0.500 A

    Animation
      No. of frames: 11
      Mean displacements (A):    0.50

    Displacement vector
      Mean length of vectors (A):    3.00