HEADER    IMMUNE SYSTEM                           12-MAY-16   5G4D              
TITLE     CRYSTAL STRUCTURE OF THE CAS2 IN T.ONNURINEUS                         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2;                   
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: CAS2                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: THERMOCOCCUS ONNURINEUS;                        
SOURCE   3 ORGANISM_TAXID: 342948                                               
KEYWDS    IMMUNE SYSTEM, CRIPSR-CAS COMPLEX, ADAPTATION                         
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    T.Y.JUNG,K.H.PARK,E.J.WOO                                             
REVDAT   3   08-MAY-24 5G4D    1       REMARK                                   
REVDAT   2   05-OCT-16 5G4D    1       JRNL                                     
REVDAT   1   27-JUL-16 5G4D    0                                                
JRNL        AUTH   T.JUNG,K.PARK,A.YAN,A.SCHULGA,S.DEYEV,J.JUNG,E.WOO           
JRNL        TITL   STRUCTURAL FEATURES OF CAS2 FROM THERMOCOCCUS ONNURINEUS IN  
JRNL        TITL 2 CRISPR-CAS SYSTEM TYPE IV.                                   
JRNL        REF    PROTEIN SCI.                  V.  25  1890 2016              
JRNL        REFN                   ISSN 0961-8368                               
JRNL        PMID   27400737                                                     
JRNL        DOI    10.1002/PRO.2981                                             
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX                                               
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) : 1.70                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.75                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.380                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.1                           
REMARK   3   NUMBER OF REFLECTIONS             : 9301                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.218                           
REMARK   3   R VALUE            (WORKING SET) : 0.215                           
REMARK   3   FREE R VALUE                     : 0.241                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 930                             
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 25.7561 -  3.2512    0.95     1231   137  0.2012 0.2202        
REMARK   3     2  3.2512 -  2.5814    1.00     1224   136  0.2271 0.2362        
REMARK   3     3  2.5814 -  2.2553    1.00     1198   134  0.2232 0.2482        
REMARK   3     4  2.2553 -  2.0492    1.00     1188   131  0.2091 0.2392        
REMARK   3     5  2.0492 -  1.9023    1.00     1189   132  0.2151 0.2611        
REMARK   3     6  1.9023 -  1.7902    1.00     1184   133  0.2283 0.2931        
REMARK   3     7  1.7902 -  1.7006    1.00     1157   127  0.2395 0.3023        
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)     : 0.180            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.670           
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      :  0.006            663                                  
REMARK   3   ANGLE     :  0.814            892                                  
REMARK   3   CHIRALITY :  0.058            102                                  
REMARK   3   PLANARITY :  0.004            112                                  
REMARK   3   DIHEDRAL  : 15.592            405                                  
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 5G4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAY-16.                  
REMARK 100 THE DEPOSITION ID IS D_1290066828.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : NULL                               
REMARK 200  TEMPERATURE           (KELVIN) : 287                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : PAL/PLS                            
REMARK 200  BEAMLINE                       : 5C (4A)                            
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1                                  
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : NULL                               
REMARK 200  DETECTOR MANUFACTURER          : NULL                               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL                               
REMARK 200  DATA SCALING SOFTWARE          : NULL                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 9301                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 27.640                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.1                               
REMARK 200  DATA REDUNDANCY                : 6.500                              
REMARK 200  R MERGE                    (I) : 0.05000                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD                          
REMARK 200 SOFTWARE USED: NULL                                                  
REMARK 200 STARTING MODEL: NONE                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NONE                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 36.59                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0                                   
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y,-Z                                                 
REMARK 290       3555   X+1/2,-Y,-Z+1/2                                         
REMARK 290       4555   -X+1/2,-Y,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 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       14.75750            
REMARK 290   SMTRY2   3  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       41.58050            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       14.75750            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       41.58050            
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: DIMERIC                           
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 8810 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.9 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 350   BIOMT1   2 -1.000000  0.000000  0.000000      -29.51500            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375      HOH A2019  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A2065  LIES ON A SPECIAL POSITION.                          
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     GLU A    77                                                      
REMARK 465     LYS A    78                                                      
REMARK 465     ASN A    79                                                      
REMARK 465     PRO A    80                                                      
REMARK 465     LEU A    81                                                      
REMARK 465     GLU A    82                                                      
REMARK 465     ASP A    83                                                      
REMARK 465     ILE A    84                                                      
REMARK 465     ILE A    85                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   O    MET A    76     O    HOH A  2062              1.91            
REMARK 500   O    HOH A  2033     O    HOH A  2035              2.07            
REMARK 500   O    HOH A  2007     O    HOH A  2024              2.14            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
REMARK 500                                                                      
REMARK 500 DISTANCE CUTOFF:                                                     
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
REMARK 500   NH1  ARG A    44     OE2  GLU A    55     3564     2.15            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 525                                                                      
REMARK 525 SOLVENT                                                              
REMARK 525                                                                      
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
REMARK 525 NUMBER; I=INSERTION CODE):                                           
REMARK 525                                                                      
REMARK 525  M RES CSSEQI                                                        
REMARK 525    HOH A2063        DISTANCE =  7.28 ANGSTROMS                       
REMARK 525    HOH A2065        DISTANCE =  7.02 ANGSTROMS                       
REMARK 525    HOH A2066        DISTANCE =  8.33 ANGSTROMS                       
DBREF  5G4D A    1    85  UNP    B6YTB8   B6YTB8_THEON     1     85             
SEQADV 5G4D ALA A   -2  UNP  B6YTB8              EXPRESSION TAG                 
SEQADV 5G4D MET A   -1  UNP  B6YTB8              EXPRESSION TAG                 
SEQADV 5G4D ASP A    0  UNP  B6YTB8              EXPRESSION TAG                 
SEQADV 5G4D ARG A   16  UNP  B6YTB8    LYS    16 CONFLICT                       
SEQRES   1 A   88  ALA MET ASP MET TYR VAL VAL ILE VAL TYR ASP VAL ALA          
SEQRES   2 A   88  VAL GLU ARG VAL ASN ARG VAL LYS LYS PHE LEU ARG ARG          
SEQRES   3 A   88  HIS LEU HIS TRP VAL GLN ASN SER VAL PHE GLU GLY GLU          
SEQRES   4 A   88  VAL THR LEU ALA GLU PHE GLU ARG ILE LYS ALA GLY LEU          
SEQRES   5 A   88  LEU ASP LEU ILE ASP GLU ASP GLU ASP SER VAL VAL ILE          
SEQRES   6 A   88  TYR LYS LEU ARG SER MET PRO LYS ARG GLU VAL LEU GLY          
SEQRES   7 A   88  MET GLU LYS ASN PRO LEU GLU ASP ILE ILE                      
FORMUL   2  HOH   *66(H2 O)                                                     
HELIX    1   1 ARG A   13  ARG A   23  1                                  11    
HELIX    2   2 THR A   38  ILE A   53  1                                  16    
SHEET    1  AA 4 HIS A  26  GLN A  29  0                                        
SHEET    2  AA 4 VAL A  32  VAL A  37 -1  O  VAL A  32   N  VAL A  28           
SHEET    3  AA 4 MET A   1  ASP A   8 -1  O  MET A   1   N  VAL A  37           
SHEET    4  AA 4 SER A  59  LEU A  65 -1  O  SER A  59   N  ASP A   8           
CRYST1   29.515   32.802   83.161  90.00  90.00  90.00 P 21 2 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      0.033881  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.030486  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.012025        0.00000