PDB Short entry for 1QXT
HEADER    LUMINESCENT PROTEIN                     08-SEP-03   1QXT              
TITLE     CRYSTAL STRUCTURE OF PRECYCLIZED INTERMEDIATE FOR THE GREEN           
TITLE    2 FLUORESCENT PROTEIN R96A VARIANT (A)                                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: GREEN-FLUORESCENT PROTEIN;                                 
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: RESIDUES 1-229;                                            
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA;                              
SOURCE   3 ORGANISM_TAXID: 6100;                                                
SOURCE   4 GENE: GFP;                                                           
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: JM109;                                     
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PKEN2                                      
KEYWDS    BETA BARREL, TRAPPED INTERMEDIATE, CHROMOPHORE, LUMINESCENT           
KEYWDS   2 PROTEIN                                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    D.P.BARONDEAU,C.D.PUTNAM,C.J.KASSMANN,J.A.TAINER,E.D.GETZOFF          
REVDAT   3   24-FEB-09 1QXT    1       VERSN                                    
REVDAT   2   14-OCT-03 1QXT    1       JRNL                                     
REVDAT   1   23-SEP-03 1QXT    0                                                
JRNL        AUTH   D.P.BARONDEAU,C.D.PUTNAM,C.J.KASSMANN,J.A.TAINER,            
JRNL        AUTH 2 E.D.GETZOFF                                                  
JRNL        TITL   MECHANISM AND ENERGETICS OF GREEN FLUORESCENT                
JRNL        TITL 2 PROTEIN CHROMOPHORE SYNTHESIS REVEALED BY TRAPPED            
JRNL        TITL 3 INTERMEDIATE STRUCTURES                                      
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 100 12111                   
JRNL        REFN                   ISSN 0027-8424                               
JRNL        PMID   14523232                                                     
JRNL        DOI    10.1073/PNAS.2133463100                                      
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.0                                              
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,             
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : ENGH & HUBER                                    
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.74                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 606673.230                     
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 93.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 14709                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.218                           
REMARK   3   FREE R VALUE                     : 0.257                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.900                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 728                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.010                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 6                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.00                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.13                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 89.40                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 2172                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2710                       
REMARK   3   BIN FREE R VALUE                    : 0.3560                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.40                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 125                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.032                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1782                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 143                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 13.80                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 28.20                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -8.72000                                             
REMARK   3    B22 (A**2) : -0.09000                                             
REMARK   3    B33 (A**2) : 8.81000                                              
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  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.24                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.21                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.31                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.27                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.012                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.60                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 28.20                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.36                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : 1.260 ; 1.500                
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 1.940 ; 2.000                
REMARK   3   SIDE-CHAIN BOND              (A**2) : 2.110 ; 2.000                
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 3.180 ; 2.500                
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.39                                                 
REMARK   3   BSOL        : 26.55                                                
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : PROTEIN.GFP.PARAM                              
REMARK   3  PARAMETER FILE  2  : WATER_REP.PARAM                                
REMARK   3  PARAMETER FILE  3  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.GFP.TOP                                
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP                                      
REMARK   3  TOPOLOGY FILE  3   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1QXT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-03.                  
REMARK 100 THE RCSB ID CODE IS RCSB020199.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 29-MAR-99                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 8.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRL                               
REMARK 200  BEAMLINE                       : BL9-1                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.78                               
REMARK 200  MONOCHROMATOR                  : CURVED CRYSTAL                     
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 15550                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.0                               
REMARK 200  DATA REDUNDANCY                : 3.530                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.06600                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 18.2000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.07                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.37200                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 3.300                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: CNS                                                   
REMARK 200 STARTING MODEL: 1EMA                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 43.36                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM CHLORIDE,            
REMARK 280  HEPES, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K      
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       25.96400            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       34.91600            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       30.78550            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       34.91600            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       25.96400            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       30.78550            
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     MET A     0                                                      
REMARK 465     ALA A     1                                                      
REMARK 465     SER A     2                                                      
REMARK 465     LYS A     3                                                      
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1QY3   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1QYF   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1QYO   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1QYQ   RELATED DB: PDB                                   
DBREF  1QXT A    1   229  UNP    P42212   GFP_AEQVI        1    229             
SEQADV 1QXT ALA A    1  UNP  P42212              CLONING ARTIFACT               
SEQADV 1QXT LEU A   64  UNP  P42212    PHE    64 ENGINEERED                     
SEQADV 1QXT THR A   65  UNP  P42212    SER    65 ENGINEERED                     
SEQADV 1QXT ALA A   96  UNP  P42212    ARG    96 ENGINEERED                     
SEQADV 1QXT SER A   99  UNP  P42212    PHE    99 ENGINEERED                     
SEQADV 1QXT THR A  153  UNP  P42212    MET   153 ENGINEERED                     
SEQADV 1QXT ALA A  163  UNP  P42212    VAL   163 ENGINEERED                     
SEQRES   1 A  230  MET ALA SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL          
SEQRES   2 A  230  PRO ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS          
SEQRES   3 A  230  LYS PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR          
SEQRES   4 A  230  TYR GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY          
SEQRES   5 A  230  LYS LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR LEU          
SEQRES   6 A  230  THR TYR GLY VAL GLN CYS PHE SER ARG TYR PRO ASP HIS          
SEQRES   7 A  230  MET LYS GLN HIS ASP PHE PHE LYS SER ALA MET PRO GLU          
SEQRES   8 A  230  GLY TYR VAL GLN GLU ALA THR ILE SER PHE LYS ASP ASP          
SEQRES   9 A  230  GLY ASN TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY          
SEQRES  10 A  230  ASP THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP          
SEQRES  11 A  230  PHE LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU          
SEQRES  12 A  230  TYR ASN TYR ASN SER HIS ASN VAL TYR ILE THR ALA ASP          
SEQRES  13 A  230  LYS GLN LYS ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG          
SEQRES  14 A  230  HIS ASN ILE GLU ASP GLY SER VAL GLN LEU ALA ASP HIS          
SEQRES  15 A  230  TYR GLN GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU          
SEQRES  16 A  230  LEU PRO ASP ASN HIS TYR LEU SER THR GLN SER ALA LEU          
SEQRES  17 A  230  SER LYS ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU          
SEQRES  18 A  230  LEU GLU PHE VAL THR ALA ALA GLY ILE                          
FORMUL   2  HOH   *143(H2 O)                                                    
HELIX    1   1 GLY A    4  THR A    9  5                                   6    
HELIX    2   2 PRO A   56  TYR A   66  1                                  11    
HELIX    3   3 GLY A   67  SER A   72  5                                   6    
HELIX    4   4 PRO A   75  HIS A   81  5                                   7    
HELIX    5   5 ASP A   82  ALA A   87  1                                   6    
SHEET    1   A12 VAL A  12  VAL A  22  0                                        
SHEET    2   A12 HIS A  25  ASP A  36 -1  O  GLY A  31   N  VAL A  16           
SHEET    3   A12 LYS A  41  CYS A  48 -1  O  LYS A  41   N  ASP A  36           
SHEET    4   A12 HIS A 217  ALA A 227 -1  O  MET A 218   N  PHE A  46           
SHEET    5   A12 HIS A 199  SER A 208 -1  N  SER A 202   O  THR A 225           
SHEET    6   A12 HIS A 148  ASP A 155 -1  N  ILE A 152   O  HIS A 199           
SHEET    7   A12 GLY A 160  ASN A 170 -1  O  GLY A 160   N  ASP A 155           
SHEET    8   A12 VAL A 176  PRO A 187 -1  O  GLN A 183   N  ALA A 163           
SHEET    9   A12 TYR A  92  PHE A 100 -1  N  VAL A  93   O  THR A 186           
SHEET   10   A12 ASN A 105  GLU A 115 -1  O  THR A 108   N  ALA A  96           
SHEET   11   A12 THR A 118  ILE A 128 -1  O  THR A 118   N  GLU A 115           
SHEET   12   A12 VAL A  12  VAL A  22  1  N  ASP A  21   O  GLY A 127           
CISPEP   1 MET A   88    PRO A   89          0        -0.17                     
CRYST1   51.928   61.571   69.832  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      0.019257  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.016241  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.014320        0.00000