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Database: PDB
Entry: 3TB8
LinkDB: 3TB8
Original site: 3TB8 
HEADER    APOPTOSIS                               05-AUG-11   3TB8              
TITLE     CRYSTAL STRUCTURE OF FULL-LENGTH MYRISTOYLATED HIV-1 NEF              
CAVEAT     3TB8    THE COORDINATES CONTAIN ONLY THE CA ATOMS                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PROTEIN NEF;                                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: 3'ORF, NEGATIVE FACTOR, F-PROTEIN, C-TERMINAL CORE PROTEIN; 
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 OTHER_DETAILS: MYRISTOYLATED                                         
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1;            
SOURCE   3 ORGANISM_COMMON: HIV-1;                                              
SOURCE   4 ORGANISM_TAXID: 11678;                                               
SOURCE   5 STRAIN: BH10;                                                        
SOURCE   6 GENE: NEF;                                                           
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    F-PROTEIN (PF00469), APOPTOSIS                                        
EXPDTA    X-RAY DIFFRACTION                                                     
MDLTYP    CA ATOMS ONLY, CHAIN A                                                
AUTHOR    C.A.DENNIS,M.HARRIS,J.JAEGER                                          
REVDAT   1   03-OCT-12 3TB8    0                                                
JRNL        AUTH   C.A.DENNIS,M.HARRIS,J.JAEGER                                 
JRNL        TITL   CRYSTAL STRUCTURE OF FULL-LENGTH MYRISTOYLATED HIV-1 NEF     
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    3.71 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.6.2_432 - REFINE                            
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : TWIN_LSQ_F                                    
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 3.71                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 28.25                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.060                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.7                           
REMARK   3   NUMBER OF REFLECTIONS             : 2622                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.233                           
REMARK   3   R VALUE            (WORKING SET) : 0.231                           
REMARK   3   FREE R VALUE                     : 0.337                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 3.280                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 86                              
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  0.0000 -  3.7100    0.96     2436    86  0.2308 0.3366        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : 0.00                                          
REMARK   3   B_SOL              : 0.18                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : NULL             
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.660           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -7.36620                                             
REMARK   3    B22 (A**2) : 11.22480                                             
REMARK   3    B33 (A**2) : -3.85870                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : -0.00000                                             
REMARK   3    B23 (A**2) : 0.00000                                              
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      :   NULL           NULL                                  
REMARK   3   ANGLE     :   NULL           NULL                                  
REMARK   3   CHIRALITY :   NULL           NULL                                  
REMARK   3   PLANARITY :   NULL           NULL                                  
REMARK   3   DIHEDRAL  :   NULL           NULL                                  
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 3TB8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-11.                  
REMARK 100 THE RCSB ID CODE IS RCSB067266.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 15-JUL-04                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : CU FINE FOCUS                      
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.54                               
REMARK 200  MONOCHROMATOR                  : YALE                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : AREA DETECTOR                      
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IV++                  
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 2622                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 3.710                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 28.250                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 1.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.7                               
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: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHENIX - PHASER                                       
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 47.92                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% POLYETHYLENEGLYCOL 3350,             
REMARK 280  LITHIUM SULFATE, HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP,       
REMARK 280  TEMPERATURE 288K                                                    
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       44.66500            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       13.89000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       44.66500            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       13.89000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       44.66500            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       44.66500            
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 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     LYS A   204                                                      
REMARK 465     ASN A   205                                                      
REMARK 465     CYS A   206                                                      
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1AVV   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1EFN   RELATED DB: PDB                                   
DBREF  3TB8 A    2   206  UNP    P03404   NEF_HV1B1        2    206             
SEQADV 3TB8 MYR A    1  UNP  P03404              MYRISTOYLATED                  
SEQRES   1 A  206  MYR GLY GLY LYS TRP SER LYS SER SER VAL ILE GLY TRP          
SEQRES   2 A  206  PRO ALA VAL ARG GLU ARG MET ARG ARG ALA GLU PRO ALA          
SEQRES   3 A  206  ALA ASP GLY VAL GLY ALA ALA SER ARG ASP LEU GLU LYS          
SEQRES   4 A  206  HIS GLY ALA ILE THR SER SER ASN THR ALA ALA ASN ASN          
SEQRES   5 A  206  ALA ALA CYS ALA TRP LEU GLU ALA GLN GLU GLU GLU LYS          
SEQRES   6 A  206  VAL GLY PHE PRO VAL THR PRO GLN VAL PRO LEU ARG PRO          
SEQRES   7 A  206  MET THR TYR LYS ALA ALA VAL ASP LEU SER HIS PHE LEU          
SEQRES   8 A  206  LYS GLU LYS GLY GLY LEU GLU GLY LEU ILE HIS SER GLN          
SEQRES   9 A  206  ARG ARG GLN ASP ILE LEU ASP LEU TRP ILE TYR HIS THR          
SEQRES  10 A  206  GLN GLY TYR PHE PRO ASP TRP GLN ASN TYR THR PRO GLY          
SEQRES  11 A  206  PRO GLY ILE ARG TYR PRO LEU THR PHE GLY TRP CYS TYR          
SEQRES  12 A  206  LYS LEU VAL PRO VAL GLU PRO ASP LYS VAL GLU GLU ALA          
SEQRES  13 A  206  ASN LYS GLY GLU ASN THR SER LEU LEU HIS PRO VAL SER          
SEQRES  14 A  206  LEU HIS GLY MET ASP ASP PRO GLU ARG GLU VAL LEU GLU          
SEQRES  15 A  206  TRP ARG PHE ASP SER ARG LEU ALA PHE HIS HIS VAL ALA          
SEQRES  16 A  206  ARG GLU LEU HIS PRO GLU TYR PHE LYS ASN CYS                  
HET    MYR  A   1       1                                                       
HETNAM     MYR MYRISTIC ACID                                                    
FORMUL   1  MYR    C14 H28 O2                                                   
CRYST1   89.330   89.330   27.780  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      0.011194  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.011194  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.035997        0.00000                         
HETATM    1  C1  MYR A   1      13.144   0.663  25.060  1.00139.80           C  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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