HEADER    DNA                                     24-APR-03   1P4Y              
TITLE     EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY     
TITLE    2 JUNCTIONS                                                            
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3';                    
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA      
SOURCE   4 SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-        
SOURCE   5 PROTECTING GROUP LEFT INTACT AT THE 5-TERMINAL NUCLEOTIDE, FOR       
SOURCE   6 SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3%  
SOURCE   7 ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM           
SOURCE   8 HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.             
KEYWDS    HOLLIDAY JUNCTION, DNA FOUR-WAY JUNCTION, DNA                         
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    F.A.HAYS,J.M.VARGASON,P.S.HO                                          
REVDAT   4   03-APR-24 1P4Y    1       REMARK                                   
REVDAT   3   14-FEB-24 1P4Y    1       REMARK LINK                              
REVDAT   2   24-FEB-09 1P4Y    1       VERSN                                    
REVDAT   1   02-SEP-03 1P4Y    0                                                
JRNL        AUTH   F.A.HAYS,J.M.VARGASON,P.S.HO                                 
JRNL        TITL   EFFECT OF SEQUENCE ON THE CONFORMATION OF DNA HOLLIDAY       
JRNL        TITL 2 JUNCTIONS                                                    
JRNL        REF    BIOCHEMISTRY                  V.  42  9586 2003              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   12911300                                                     
JRNL        DOI    10.1021/BI0346603                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.0                                              
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) : 1.70                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 22.50                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 77.1                           
REMARK   3   NUMBER OF REFLECTIONS             : 4436                           
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) : 0.229                           
REMARK   3   FREE R VALUE                     : 0.260                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 490                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.012                           
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) : 1.70                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.81                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 40.80                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 374                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2090                       
REMARK   3   BIN FREE R VALUE                    : 0.2850                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 9.40                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 39                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.046                        
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          : 4                                       
REMARK   3   SOLVENT ATOMS            : 108                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 1.60                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 8.70                           
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  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.21                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.03                            
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) : 0.26                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.10                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.007                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.200                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 18.50                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.570                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : NULL                                      
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 : NULL                                                 
REMARK   3   KSOL        : NULL                                                 
REMARK   3   BSOL        : NULL                                                 
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  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1P4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-03.                  
REMARK 100 THE DEPOSITION ID IS D_1000019012.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 24-JAN-03                          
REMARK 200  TEMPERATURE           (KELVIN) : 103.0                              
REMARK 200  PH                             : 7.00                               
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 RU300                       
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.542                              
REMARK 200  MONOCHROMATOR                  : NI FILTER                          
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IV                    
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 4940                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.650                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 22.550                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 74.0                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : 0.04800                            
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) : 1.65                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.71                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 21.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.27900                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.140                              
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: UD0008                                               
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 35.95                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5MM DNA, 25MM SODIUM CACODYLATE,       
REMARK 280  7.5MM CACL2, 0.1MM SPERMINE TETRAHYDROCHLORIDE, PH 7.0, VAPOR       
REMARK 280  DIFFUSION, SITTING DROP, TEMPERATURE 298K, PH 7.00                  
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       33.25650            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       12.08950            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       33.25650            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       12.08950            
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 300 REMARK: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT     
REMARK 300 WHICH CONSISTS OF TWO CHAINS A AND B. THE FULL FOUR STRANDED         
REMARK 300 HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING:       
REMARK 300 MATRIX= ( -1.00000 -0.00046 -0.00015 ) ( -0.00046 1.00000 0.00072 )  
REMARK 300 ( 0.00015 0.00072 -1.00000 ) TRANSLATION= (-12.65734 -0.02663        
REMARK 300 34.77174)                                                            
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      -12.66218            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       34.77018            
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA A  36  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DC A   1   O5'                                                    
REMARK 620 2 HOH A  82   O   121.7                                              
REMARK 620 N                    1                                               
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA A  49  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DG A  10   N3                                                     
REMARK 620 2 HOH A  56   O   101.5                                              
REMARK 620 N                    1                                               
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA A  21  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HOH A  24   O                                                      
REMARK 620 2 HOH A  25   O    77.2                                              
REMARK 620 3 HOH A  56   O    83.5 147.8                                        
REMARK 620 4 HOH A 109   O   134.8 143.1  66.6                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA B  55  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DG B  19   O4'                                                    
REMARK 620 2 HOH B  75   O    57.0                                              
REMARK 620 N                    1                                               
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 21                   
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 36                   
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 49                   
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 55                   
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1P4Z   RELATED DB: PDB                                   
REMARK 900 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY    
REMARK 900 JUNCTIONS                                                            
REMARK 900 RELATED ID: 1P54   RELATED DB: PDB                                   
REMARK 900 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY    
REMARK 900 JUNCTIONS                                                            
DBREF  1P4Y A    1    10  PDB    1P4Y     1P4Y             1     10             
DBREF  1P4Y B   11    20  PDB    1P4Y     1P4Y            11     20             
SEQRES   1 A   10   DC  DC  DG  DG  DC  DG  DC  DC  DG  DG                      
SEQRES   1 B   10   DC  DC  DG  DG  DC  DG  DC  DC  DG  DG                      
HET     NA  A  21       1                                                       
HET     NA  A  36       1                                                       
HET     NA  A  49       1                                                       
HET     NA  B  55       1                                                       
HETNAM      NA SODIUM ION                                                       
FORMUL   3   NA    4(NA 1+)                                                     
FORMUL   7  HOH   *108(H2 O)                                                    
LINK         O5'  DC A   1                NA    NA A  36     1555   1555  2.48  
LINK         N3   DG A  10                NA    NA A  49     1555   1555  2.95  
LINK        NA    NA A  21                 O   HOH A  24     1555   1555  2.81  
LINK        NA    NA A  21                 O   HOH A  25     1555   1555  2.47  
LINK        NA    NA A  21                 O   HOH A  56     1555   1555  2.72  
LINK        NA    NA A  21                 O   HOH A 109     1555   1555  2.48  
LINK        NA    NA A  36                 O   HOH A  82     1555   1555  2.64  
LINK        NA    NA A  49                 O   HOH A  56     1555   1555  2.56  
LINK         O4'  DG B  19                NA    NA B  55     1555   1555  2.63  
LINK        NA    NA B  55                 O   HOH B  75     1555   1555  2.81  
SITE     1 AC1  6 HOH A  24  HOH A  25   NA A  49  HOH A  56                    
SITE     2 AC1  6 HOH A 109  HOH B  76                                          
SITE     1 AC2  4  DC A   1   DC A   2  HOH A  82   DG B  14                    
SITE     1 AC3  3  DG A  10   NA A  21  HOH A  56                               
SITE     1 AC4  2  DG B  19  HOH B  75                                          
CRYST1   66.513   24.179   37.004  90.00 110.01  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      0.015035  0.000000  0.005475        0.00000                         
SCALE2      0.000000  0.041358  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.028760        0.00000