HEADER    DNA                                     06-JAN-04   1S1L              
TITLE     INFLUENCE OF GROOVE INTERACTIONS ON THE FORMATION OF DNA HOLLIDAY     
TITLE    2 JUNCTIONS                                                            
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3';             
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    HOLLIDAY JUNCTION, DNA FOUR-WAY JUNCTION, MAJOR GROOVE, INOSINE,      
KEYWDS   2 MINOR GROOVE, DNA                                                    
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    F.A.HAYS,Z.J.JONES,P.S.HO                                             
REVDAT   5   03-APR-24 1S1L    1       REMARK                                   
REVDAT   4   14-FEB-24 1S1L    1       LINK                                     
REVDAT   3   11-OCT-17 1S1L    1       REMARK                                   
REVDAT   2   24-FEB-09 1S1L    1       VERSN                                    
REVDAT   1   31-AUG-04 1S1L    0                                                
JRNL        AUTH   F.A.HAYS,Z.J.JONES,P.S.HO                                    
JRNL        TITL   INFLUENCE OF MINOR GROOVE SUBSTITUENTS ON THE STRUCTURE OF   
JRNL        TITL 2 DNA HOLLIDAY JUNCTIONS.                                      
JRNL        REF    BIOCHEMISTRY                  V.  43  9813 2004              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   15274635                                                     
JRNL        DOI    10.1021/BI049461D                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.20 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.1                                              
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : NULL                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 18.20                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 44978.750                      
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 96.2                           
REMARK   3   NUMBER OF REFLECTIONS             : 2852                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.236                           
REMARK   3   FREE R VALUE                     : 0.258                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 286                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.015                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 6                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.20                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.34                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 88.00                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 391                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2670                       
REMARK   3   BIN FREE R VALUE                    : 0.3340                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 9.30                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 40                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.053                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 0                                       
REMARK   3   NUCLEIC ACID ATOMS       : 404                                     
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 62                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 11.20                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 11.20                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 2.08000                                              
REMARK   3    B22 (A**2) : 2.33000                                              
REMARK   3    B33 (A**2) : -4.41000                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : -1.93000                                             
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.28                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.16                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.29                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.37                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.003                           
REMARK   3   BOND ANGLES            (DEGREES) : 0.800                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 18.40                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.280                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.36                                                 
REMARK   3   BSOL        : 50.37                                                
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : DNA-RNA_REP.PARAM                              
REMARK   3  PARAMETER FILE  2  : ION.PARAM                                      
REMARK   3  PARAMETER FILE  3  : WATER_REP.PARAM                                
REMARK   3  PARAMETER FILE  4  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : DNA-RNA.TOP                                    
REMARK   3  TOPOLOGY FILE  2   : ION.TOP                                        
REMARK   3  TOPOLOGY FILE  3   : WATER.TOP                                      
REMARK   3  TOPOLOGY FILE  4   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1S1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-04.                  
REMARK 100 THE DEPOSITION ID IS D_1000021251.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 08-NOV-03                          
REMARK 200  TEMPERATURE           (KELVIN) : 103                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU                             
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.542                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : OSMIC MIRRORS                      
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IV                    
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : R-AXIS                             
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 3492                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 18.200                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 93.4                               
REMARK 200  DATA REDUNDANCY                : NULL                               
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) : 2.00                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.07                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 61.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.29100                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.400                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: EPMR                                                  
REMARK 200 STARTING MODEL: NDB ID UD0019                                        
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 42.80                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 25MM NA CACODYLATE, .5MM DNA, 180MM      
REMARK 280  CACL2, 2.4MM SPERMINE AGAINST 20% RESEVOIR MPD, PH 7.0, VAPOR       
REMARK 280  DIFFUSION, SITTING DROP                                             
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1                          
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+1/2,Z                                           
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        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       32.46150            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       12.43450            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       32.46150            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       12.43450            
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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT             
REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). THE FULL BIOLOGICAL UNIT               
REMARK 300 CONSISTS OF A FOUR STRANDED DNA HOLLIDAY JUNCTION. SEE               
REMARK 300 REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL              
REMARK 300 MOLECULE(S).                                                         
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: TETRAMERIC                        
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B                                  
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       52.71146            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       35.02738            
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 B  49  LIES ON A SPECIAL POSITION.                          
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   O    HOH B    42     O    HOH B    42     2655     1.47            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: UD0006   RELATED DB: NDB                                 
REMARK 900 DNA HOLLIDAY JUNCTION                                                
REMARK 900 RELATED ID: UD0008   RELATED DB: NDB                                 
REMARK 900 DNA HOLLIDAY JUNCTION                                                
REMARK 900 RELATED ID: UD0019   RELATED DB: NDB                                 
REMARK 900 DNA HOLLIDAY JUNCTION                                                
REMARK 900 RELATED ID: UD0028   RELATED DB: NDB                                 
REMARK 900 DNA HOLLIDAY JUNCTION                                                
REMARK 900 RELATED ID: UD0030   RELATED DB: NDB                                 
REMARK 900 DNA HOLLIDAY JUNCTION                                                
DBREF  1S1L A    1    10  PDB    1S1L     1S1L             1     10             
DBREF  1S1L B    1    10  PDB    1S1L     1S1L             1     10             
SEQRES   1 A   10   DC  DC  DI  DG  DT  DA  DC 5CM  DG  DG                      
SEQRES   1 B   10   DC  DC  DI  DG  DT  DA  DC 5CM  DG  DG                      
MODRES 1S1L 5CM A    8   DC                                                     
MODRES 1S1L 5CM B    8   DC                                                     
HET    5CM  A   8      20                                                       
HET    5CM  B   8      20                                                       
HETNAM     5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE                      
FORMUL   1  5CM    2(C10 H16 N3 O7 P)                                           
FORMUL   3  HOH   *62(H2 O)                                                     
LINK         O3'  DC A   7                 P   5CM A   8     1555   1555  1.60  
LINK         O3' 5CM A   8                 P    DG A   9     1555   1555  1.60  
LINK         O3'  DC B   7                 P   5CM B   8     1555   1555  1.60  
LINK         O3' 5CM B   8                 P    DG B   9     1555   1555  1.60  
CRYST1   64.923   24.869   37.095  90.00 109.22  90.00 C 1 2 1       8          
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      0.015403  0.000000  0.005370        0.00000                         
SCALE2      0.000000  0.040211  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.028549        0.00000