PDB Short entry for 6EXT
HEADER    DNA BINDING PROTEIN                     09-NOV-17   6EXT              
TITLE     CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF FISSION YEAST SAP1     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: SWITCH-ACTIVATING PROTEIN 1;                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC    
SOURCE   3 24843);                                                              
SOURCE   4 ORGANISM_COMMON: FISSION YEAST;                                      
SOURCE   5 ORGANISM_TAXID: 284812;                                              
SOURCE   6 STRAIN: 972 / ATCC 24843;                                            
SOURCE   7 GENE: SAP1, SPCC1672.02C;                                            
SOURCE   8 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   9 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE  10 EXPRESSION_SYSTEM_STRAIN: C2566                                      
KEYWDS    S. POMBE, MATING TYPE SWITCH, DNA REPLICATION, MYB DOMAIN, DNA        
KEYWDS   2 BINDING PROTEIN                                                      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    B.EKUNDAYO,M.JOERGENSEN,T.SCHALCH                                     
REVDAT   2   17-JAN-24 6EXT    1       REMARK                                   
REVDAT   1   28-NOV-18 6EXT    0                                                
JRNL        AUTH   M.M.JORGENSEN,B.EKUNDAYO,M.ZARATIEGUI,K.SKRIVER,G.THON,      
JRNL        AUTH 2 T.SCHALCH                                                    
JRNL        TITL   STRUCTURE OF THE REPLICATION REGULATOR SAP1 REVEALS          
JRNL        TITL 2 FUNCTIONALLY IMPORTANT INTERFACES.                           
JRNL        REF    SCI REP                       V.   8 10930 2018              
JRNL        REFN                   ESSN 2045-2322                               
JRNL        PMID   30026545                                                     
JRNL        DOI    10.1038/S41598-018-29198-9                                   
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (1.12_2829: ???)                              
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 : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.61                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0                          
REMARK   3   NUMBER OF REFLECTIONS             : 17121                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.169                           
REMARK   3   R VALUE            (WORKING SET) : 0.169                           
REMARK   3   FREE R VALUE                     : 0.212                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 7.670                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1314                            
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 35.6240 -  3.1196    1.00     1887   157  0.1681 0.1799        
REMARK   3     2  3.1196 -  2.4763    1.00     1777   147  0.1641 0.1986        
REMARK   3     3  2.4763 -  2.1634    1.00     1756   147  0.1521 0.1698        
REMARK   3     4  2.1634 -  1.9656    1.00     1754   146  0.1516 0.2001        
REMARK   3     5  1.9656 -  1.8247    1.00     1739   145  0.1688 0.2097        
REMARK   3     6  1.8247 -  1.7171    1.00     1741   144  0.1689 0.2038        
REMARK   3     7  1.7171 -  1.6311    1.00     1710   143  0.1692 0.1990        
REMARK   3     8  1.6311 -  1.5601    1.00     1726   143  0.1627 0.2042        
REMARK   3     9  1.5601 -  1.5001    1.00     1717   142  0.1737 0.2203        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
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)     : 0.120            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.850           
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) : 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      :  0.009            897                                  
REMARK   3   ANGLE     :  1.084           1204                                  
REMARK   3   CHIRALITY :  0.209            130                                  
REMARK   3   PLANARITY :  0.006            156                                  
REMARK   3   DIHEDRAL  : 16.106            563                                  
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 6EXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-NOV-17.                  
REMARK 100 THE DEPOSITION ID IS D_1200007424.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 08-SEP-14                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X06SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0                                
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 2M-F               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : AIMLESS                            
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 17123                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 35.610                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY                : 2.000                              
REMARK 200  R MERGE                    (I) : 0.02304                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 5.6400                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.55                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.12340                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 6.210                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: 6EXU                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 34.29                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 5% W/V PEG 1500 AND PCTP BUFFER PH 7.0   
REMARK 280  (PROPIONIC ACID, CACODYLATE AND BIS-TRIS PROPANE), VAPOR            
REMARK 280  DIFFUSION, SITTING DROP, TEMPERATURE 291.0K                         
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       17.71100            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       35.61400            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       20.38650            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       35.61400            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       17.71100            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       20.38650            
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2                             
REMARK 350 SURFACE AREA OF THE COMPLEX: 7300 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL                          
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     LEU A    18                                                      
REMARK 465     SER A    19                                                      
REMARK 465     PRO A    20                                                      
REMARK 465     SER A    21                                                      
REMARK 465     SER A    22                                                      
REMARK 465     SER A    23                                                      
REMARK 465     PRO A    24                                                      
REMARK 465     ALA A    25                                                      
REMARK 465     LYS A    26                                                      
REMARK 465     ALA A    27                                                      
REMARK 465     GLN A    28                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     ARG A  29    CG   CD   NE   CZ   NH1  NH2                        
DBREF  6EXT A   18   133  UNP    P40847   SAP1_SCHPO      18    133             
SEQRES   1 A  116  LEU SER PRO SER SER SER PRO ALA LYS ALA GLN ARG THR          
SEQRES   2 A  116  HIS LEU SER LEU GLU GLU LYS ILE LYS LEU MSE ARG LEU          
SEQRES   3 A  116  VAL VAL ARG HIS LYS HIS GLU LEU VAL ASP ARG LYS THR          
SEQRES   4 A  116  SER GLU PHE TYR ALA LYS ILE ALA ARG ILE GLY TYR GLU          
SEQRES   5 A  116  ASP GLU GLY LEU ALA ILE HIS THR GLU SER ALA CYS ARG          
SEQRES   6 A  116  ASN GLN ILE ILE SER ILE MSE ARG VAL TYR GLU GLN ARG          
SEQRES   7 A  116  LEU ALA HIS ARG GLN PRO GLY MSE LYS THR THR PRO GLU          
SEQRES   8 A  116  GLU ASP GLU LEU ASP GLN LEU CYS ASP GLU TRP LYS ALA          
SEQRES   9 A  116  ARG LEU SER GLU LEU GLN GLN TYR ARG GLU LYS PHE              
MODRES 6EXT MSE A   41  MET  MODIFIED RESIDUE                                   
MODRES 6EXT MSE A   89  MET  MODIFIED RESIDUE                                   
MODRES 6EXT MSE A  103  MET  MODIFIED RESIDUE                                   
HET    MSE  A  41      17                                                       
HET    MSE  A  89      17                                                       
HET    MSE  A 103      17                                                       
HETNAM     MSE SELENOMETHIONINE                                                 
FORMUL   1  MSE    3(C5 H11 N O2 SE)                                            
FORMUL   2  HOH   *140(H2 O)                                                    
HELIX    1 AA1 SER A   33  HIS A   47  1                                  15    
HELIX    2 AA2 LYS A   48  LEU A   51  5                                   4    
HELIX    3 AA3 LYS A   55  GLY A   72  1                                  18    
HELIX    4 AA4 THR A   77  ARG A   99  1                                  23    
HELIX    5 AA5 THR A  106  PHE A  133  1                                  28    
LINK         C   LEU A  40                 N   MSE A  41     1555   1555  1.34  
LINK         C   MSE A  41                 N   ARG A  42     1555   1555  1.34  
LINK         C   ILE A  88                 N   MSE A  89     1555   1555  1.33  
LINK         C   MSE A  89                 N   ARG A  90     1555   1555  1.34  
LINK         C   GLY A 102                 N   MSE A 103     1555   1555  1.33  
LINK         C   MSE A 103                 N   LYS A 104     1555   1555  1.33  
CRYST1   35.422   40.773   71.228  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      0.028231  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.024526  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.014039        0.00000