HEADER    SIGNALING PROTEIN                       03-NOV-21   7SPX              
TITLE     CRYSTAL STRUCTURE OF PHOTOACTIVE YELLOW PROTEIN (PYP); F28OCNF        
TITLE    2 CONSTRUCT                                                            
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN;                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: PYP;                                                        
COMPND   5 ENGINEERED: 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 STR. K-12 SUBSTR. DH10B;         
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 316385;                                     
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: DH10B                                      
KEYWDS    PHOTORECEPTOR, SIGNALING PROTEIN                                      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.B.WEAVER,J.M.KIRSH,S.G.BOXER                                        
REVDAT   5   15-NOV-23 7SPX    1       LINK                                     
REVDAT   4   18-OCT-23 7SPX    1       REMARK                                   
REVDAT   3   17-AUG-22 7SPX    1       AUTHOR                                   
REVDAT   2   18-MAY-22 7SPX    1       JRNL                                     
REVDAT   1   11-MAY-22 7SPX    0                                                
JRNL        AUTH   J.B.WEAVER,J.KOZUCH,J.M.KIRSH,S.G.BOXER                      
JRNL        TITL   NITRILE INFRARED INTENSITIES CHARACTERIZE ELECTRIC FIELDS    
JRNL        TITL 2 AND HYDROGEN BONDING IN PROTIC, APROTIC, AND PROTEIN         
JRNL        TITL 3 ENVIRONMENTS.                                                
JRNL        REF    J.AM.CHEM.SOC.                V. 144  7562 2022              
JRNL        REFN                   ESSN 1520-5126                               
JRNL        PMID   35467853                                                     
JRNL        DOI    10.1021/JACS.2C00675                                         
REMARK   2                                                                      
REMARK   2 RESOLUTION.    0.97 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.19.2_4158                                   
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 33.12                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.360                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 59876                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.145                           
REMARK   3   R VALUE            (WORKING SET) : 0.144                           
REMARK   3   FREE R VALUE                     : 0.166                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.110                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 3059                            
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 33.1200 -  2.7100    1.00     2699   140  0.1529 0.1775        
REMARK   3     2  2.7100 -  2.1500    1.00     2677    99  0.1621 0.1885        
REMARK   3     3  2.1500 -  1.8800    1.00     2610   161  0.1403 0.1827        
REMARK   3     4  1.8800 -  1.7100    1.00     2617   139  0.1495 0.1542        
REMARK   3     5  1.7100 -  1.5800    1.00     2590   165  0.1251 0.1411        
REMARK   3     6  1.5800 -  1.4900    1.00     2603   144  0.1300 0.1358        
REMARK   3     7  1.4900 -  1.4200    1.00     2603   147  0.1233 0.1547        
REMARK   3     8  1.4200 -  1.3500    1.00     2605   139  0.1260 0.1482        
REMARK   3     9  1.3500 -  1.3000    1.00     2610   144  0.1202 0.1386        
REMARK   3    10  1.3000 -  1.2600    1.00     2619   113  0.1203 0.1470        
REMARK   3    11  1.2600 -  1.2200    1.00     2590   158  0.1169 0.1530        
REMARK   3    12  1.2200 -  1.1800    1.00     2590   144  0.1230 0.1365        
REMARK   3    13  1.1800 -  1.1500    1.00     2605   138  0.1187 0.1520        
REMARK   3    14  1.1500 -  1.1200    1.00     2570   144  0.1230 0.1528        
REMARK   3    15  1.1200 -  1.1000    1.00     2597   149  0.1192 0.1666        
REMARK   3    16  1.1000 -  1.0700    1.00     2596   143  0.1289 0.1341        
REMARK   3    17  1.0700 -  1.0500    1.00     2589   159  0.1408 0.1502        
REMARK   3    18  1.0500 -  1.0300    1.00     2571   143  0.1546 0.2002        
REMARK   3    19  1.0300 -  1.0100    1.00     2593   133  0.1781 0.2179        
REMARK   3    20  1.0100 -  1.0000    1.00     2629   119  0.1969 0.1977        
REMARK   3    21  1.0000 -  0.9800    1.00     2603   122  0.2369 0.2562        
REMARK   3    22  0.9800 -  0.9700    0.79     2051   116  0.2744 0.3032        
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              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.090            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.250           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 7.68                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 11.66                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
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 7SPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-21.                  
REMARK 100 THE DEPOSITION ID IS D_1000258741.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 03-JUN-21                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 6.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRL                               
REMARK 200  BEAMLINE                       : BL12-2                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.7749                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XSCALE                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 59975                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.970                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.640                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.2                               
REMARK 200  DATA REDUNDANCY                : 13.10                              
REMARK 200  R MERGE                    (I) : 0.08100                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 17.6000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.98                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 83.1                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 9.50                               
REMARK 200  R MERGE FOR SHELL          (I) : 1.81300                            
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                                                
REMARK 200 STARTING MODEL: 1NWZ                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 32.44                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE, PH 6.0, 1 M   
REMARK 280  NACL; 2.2 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP,        
REMARK 280  TEMPERATURE 293K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63                             
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z                                                
REMARK 290       3555   -X+Y,-X,Z                                               
REMARK 290       4555   -X,-Y,Z+1/2                                             
REMARK 290       5555   Y,-X+Y,Z+1/2                                            
REMARK 290       6555   X-Y,X,Z+1/2                                             
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        0.00000            
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        0.00000            
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       20.31850            
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       20.31850            
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       20.31850            
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
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     1                                                      
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    LYS A  17       18.44     58.10                                   
REMARK 500    TYR A  42      117.81   -162.20                                   
REMARK 500    ASP A  65      -61.85   -108.49                                   
REMARK 500    ASP A  65      -50.61   -126.81                                   
REMARK 500    PHE A  75      -76.88   -131.82                                   
REMARK 500    ASN A  89       90.67   -163.61                                   
REMARK 500    ASP A  97       15.14   -140.49                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  7SPX A    1   125  UNP    P16113   PYP_HALHA        1    125             
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 9IJ GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN ILE          
SEQRES   4 A  125  LEU GLN TYR ASN ALA ALA GLU 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                              
MODRES 7SPX 9IJ A   28  PHE  MODIFIED RESIDUE                                   
HET    9IJ  A  28      26                                                       
HET    HC4  A 201      11                                                       
HETNAM     9IJ 2-CYANO-L-PHENYLALANINE                                          
HETNAM     HC4 4'-HYDROXYCINNAMIC ACID                                          
HETSYN     HC4 PARA-COUMARIC ACID                                               
FORMUL   1  9IJ    C10 H10 N2 O2                                                
FORMUL   2  HC4    C9 H8 O3                                                     
FORMUL   3  HOH   *109(H2 O)                                                    
HELIX    1 AA1 ASP A   10  ALA A   16  1                                   7    
HELIX    2 AA2 ASP A   19  ASP A   24  1                                   6    
HELIX    3 AA3 ASN A   43  GLY A   51  1                                   9    
HELIX    4 AA4 ALA A   67  ASP A   71  5                                   5    
HELIX    5 AA5 PHE A   75  GLY A   86  1                                  12    
SHEET    1 AA1 5 ILE A  39  TYR A  42  0                                        
SHEET    2 AA1 5 GLY A  29  LEU A  33 -1  N  GLN A  32   O  LEU A  40           
SHEET    3 AA1 5 TYR A 118  ARG A 124 -1  O  TYR A 118   N  LEU A  33           
SHEET    4 AA1 5 THR A 103  LYS A 111 -1  N  HIS A 108   O  PHE A 121           
SHEET    5 AA1 5 ASN A  89  PHE A  96 -1  N  PHE A  92   O  VAL A 107           
LINK         C   ALA A  27                 N  A9IJ A  28     1555   1555  1.34  
LINK         C   ALA A  27                 N  B9IJ A  28     1555   1555  1.34  
LINK         C  A9IJ A  28                 N   GLY A  29     1555   1555  1.33  
LINK         C  B9IJ A  28                 N   GLY A  29     1555   1555  1.33  
LINK         SG  CYS A  69                 C1  HC4 A 201     1555   1555  1.78  
CRYST1   66.028   66.028   40.637  90.00  90.00 120.00 P 63          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      0.015145  0.008744  0.000000        0.00000                         
SCALE2      0.000000  0.017488  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.024608        0.00000