PDB Short entry for 1OTI
HEADER    SIGNALING PROTEIN                       21-MAR-03   1OTI              
TITLE     E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 295K                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN;                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: PYP;                                                        
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA;                       
SOURCE   3 ORGANISM_TAXID: 1053;                                                
SOURCE   4 GENE: PYP;                                                           
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    PYP, SIGNALING PROTEIN                                                
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.ANDERSON,S.CROSSON,K.MOFFAT                                         
REVDAT   5   27-OCT-21 1OTI    1       REMARK SEQADV                            
REVDAT   4   24-JUL-19 1OTI    1       REMARK LINK                              
REVDAT   3   24-FEB-09 1OTI    1       VERSN                                    
REVDAT   2   15-JUN-04 1OTI    1       JRNL                                     
REVDAT   1   11-MAY-04 1OTI    0                                                
JRNL        AUTH   S.ANDERSON,S.CROSSON,K.MOFFAT                                
JRNL        TITL   SHORT HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN.          
JRNL        REF    ACTA CRYSTALLOGR.,SECT.D      V.  60  1008 2004              
JRNL        REFN                   ISSN 0907-4449                               
JRNL        PMID   15159559                                                     
JRNL        DOI    10.1107/S090744490400616X                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.40 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) : 1.40                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : NULL                           
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
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) : 0.133                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.133                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.161                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 1074                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 21402                  
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL                   
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)) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : NULL                   
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 976                                           
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 11                                            
REMARK   3   SOLVENT ATOMS      : 117                                           
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL                    
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL                    
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL                    
REMARK   3   NUMBER OF RESTRAINTS                     : NULL                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.014                   
REMARK   3   ANGLE DISTANCES                      (A) : 2.550                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL                    
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL                    
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL                    
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL                    
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL                    
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL                    
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL                    
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL                    
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: NULL                                                  
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : DERIVED FROM 0.95A 110K E46Q        
REMARK   3                                  MUTANT GROUND STATE STRUCTURE       
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1OTI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-03.                  
REMARK 100 THE DEPOSITION ID IS D_1000018652.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 15-MAY-01                          
REMARK 200  TEMPERATURE           (KELVIN) : 295                                
REMARK 200  PH                             : 6.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 14-BM-C                            
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9                                
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 21402                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.400                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 100.000                            
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.4                               
REMARK 200  DATA REDUNDANCY                : 23.10                              
REMARK 200  R MERGE                    (I) : 0.08800                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 12.4000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.45                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.56800                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.600                              
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: PDB ENTRY 2PHY                                       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 39.91                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, MES, PH 6.5, VAPOR             
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 295K                           
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65                             
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z+2/3                                            
REMARK 290       3555   -X+Y,-X,Z+1/3                                           
REMARK 290       4555   -X,-Y,Z+1/2                                             
REMARK 290       5555   Y,-X+Y,Z+1/6                                            
REMARK 290       6555   X-Y,X,Z+5/6                                             
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 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       78.18467            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       39.09233            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       58.63850            
REMARK 290   SMTRY1   5  0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   5 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       19.54617            
REMARK 290   SMTRY1   6  0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       97.73083            
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    ASP A  20   CB  -  CG  -  OD1 ANGL. DEV. =   6.4 DEGREES          
REMARK 500    ASP A  36   CB  -  CG  -  OD2 ANGL. DEV. =  -6.4 DEGREES          
REMARK 500    LYS A  64   CD  -  CE  -  NZ  ANGL. DEV. =  23.1 DEGREES          
REMARK 500    ASP A  65   CB  -  CG  -  OD2 ANGL. DEV. =   8.2 DEGREES          
REMARK 500    TYR A  76   CB  -  CG  -  CD2 ANGL. DEV. =  -4.5 DEGREES          
REMARK 500    TYR A  76   CB  -  CG  -  CD1 ANGL. DEV. =   4.2 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    PHE A  75      -77.74   -130.82                                   
REMARK 500    ASN A  89       94.45   -167.05                                   
REMARK 500    ASP A  97       18.42   -143.63                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HC4 A 169                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2PHY   RELATED DB: PDB                                   
REMARK 900 PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED)                  
REMARK 900 RELATED ID: 1OTA   RELATED DB: PDB                                   
REMARK 900 E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K               
REMARK 900 RELATED ID: 1OTB   RELATED DB: PDB                                   
REMARK 900 WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K                    
REMARK 900 RELATED ID: 1OTD   RELATED DB: PDB                                   
REMARK 900 STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE   
REMARK 900 IN ITS PHOTOCYCLE                                                    
REMARK 900 RELATED ID: 1OTE   RELATED DB: PDB                                   
REMARK 900 E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 110K               
DBREF  1OTI A    1   125  UNP    P16113   PYP_ECTHA        1    125             
SEQADV 1OTI GLN A   46  UNP  P16113    GLU    46 ENGINEERED MUTATION            
SEQRES   1 A  125  MET GLU HIS VAL ALA PHE GLY SER GLU ASP ILE GLU ASN          
SEQRES   2 A  125  THR LEU ALA LYS MET ASP ASP GLY GLN LEU ASP GLY LEU          
SEQRES   3 A  125  ALA PHE GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN ILE          
SEQRES   4 A  125  LEU GLN TYR ASN ALA ALA GLN GLY ASP ILE THR GLY ARG          
SEQRES   5 A  125  ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE PHE LYS ASP          
SEQRES   6 A  125  VAL ALA PRO CYS THR ASP SER PRO GLU PHE TYR GLY LYS          
SEQRES   7 A  125  PHE LYS GLU GLY VAL ALA SER GLY ASN LEU ASN THR MET          
SEQRES   8 A  125  PHE GLU TYR THR PHE ASP TYR GLN MET THR PRO THR LYS          
SEQRES   9 A  125  VAL LYS VAL HIS MET LYS LYS ALA LEU SER GLY ASP SER          
SEQRES  10 A  125  TYR TRP VAL PHE VAL LYS ARG VAL                              
HET    HC4  A 169      11                                                       
HETNAM     HC4 4'-HYDROXYCINNAMIC ACID                                          
HETSYN     HC4 PARA-COUMARIC ACID                                               
FORMUL   2  HC4    C9 H8 O3                                                     
FORMUL   3  HOH   *117(H2 O)                                                    
HELIX    1   1 ASP A   10  LYS A   17  1                                   8    
HELIX    2   2 ASP A   19  ASP A   24  1                                   6    
HELIX    3   3 ASN A   43  GLY A   51  1                                   9    
HELIX    4   4 ASP A   53  ILE A   58  1                                   6    
HELIX    5   5 ALA A   67  ASP A   71  5                                   5    
HELIX    6   6 PHE A   75  GLY A   86  1                                  12    
SHEET    1   A 5 ILE A  39  TYR A  42  0                                        
SHEET    2   A 5 GLY A  29  LEU A  33 -1  N  GLN A  32   O  LEU A  40           
SHEET    3   A 5 TYR A 118  ARG A 124 -1  O  TYR A 118   N  LEU A  33           
SHEET    4   A 5 THR A 103  LYS A 111 -1  N  LYS A 110   O  TRP A 119           
SHEET    5   A 5 ASN A  89  PHE A  96 -1  N  PHE A  92   O  VAL A 107           
LINK         SG  CYS A  69                 C1  HC4 A 169     1555   1555  1.74  
SITE     1 AC1  8 TYR A  42  GLN A  46  THR A  50  ALA A  67                    
SITE     2 AC1  8 PRO A  68  CYS A  69  PHE A  96  TYR A  98                    
CRYST1   40.987   40.987  117.277  90.00  90.00 120.00 P 65          6          
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      0.024398  0.014086  0.000000        0.00000                         
SCALE2      0.000000  0.028172  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.008527        0.00000