HEADER    DNA, RNA                                26-JUL-01   1JO2              
TITLE     CRYSTAL STRUCTURE OF THE B-DNA HEXAMER (CGATCG).DAUNOMYCIN COMPLEX    
TITLE    2 CONTAINING A RIBOSE AT THE INTERCALATION SITE                        
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3';                        
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    INTERCALATION, DNA/RNA CHIMER, DNA, RNA                               
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    K.SHI,B.PAN,M.SUNDARALINGAM                                           
REVDAT   4   07-FEB-24 1JO2    1       REMARK                                   
REVDAT   3   04-OCT-17 1JO2    1       REMARK                                   
REVDAT   2   24-FEB-09 1JO2    1       VERSN                                    
REVDAT   1   29-JUL-03 1JO2    0                                                
JRNL        AUTH   K.SHI,B.PAN,M.SUNDARALINGAM                                  
JRNL        TITL   STRUCTURE OF A B-FORM DNA/RNA CHIMERA (DC)(RG)D(ATCG)        
JRNL        TITL 2 COMPLEXED WITH DAUNOMYCIN AT 1.5 A RESOLUTION.               
JRNL        REF    ACTA CRYSTALLOGR.,SECT.D      V.  59  1377 2003              
JRNL        REFN                   ISSN 0907-4449                               
JRNL        PMID   12876339                                                     
JRNL        DOI    10.1107/S0907444903011788                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
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) : 1.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 2.000                          
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 2.0000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 74.3                           
REMARK   3   NUMBER OF REFLECTIONS             : 2699                           
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) : 0.198                           
REMARK   3   FREE R VALUE                     : 0.233                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 256                             
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) : 1.50                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.59                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 21.20                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 112                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2860                       
REMARK   3   BIN FREE R VALUE                    : 0.2580                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 10.40                        
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 13                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.072                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 0                                       
REMARK   3   NUCLEIC ACID ATOMS       : 121                                     
REMARK   3   HETEROGEN ATOMS          : 38                                      
REMARK   3   SOLVENT ATOMS            : 40                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 14.60                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 22.10                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 0.12000                                              
REMARK   3    B22 (A**2) : 0.12000                                              
REMARK   3    B33 (A**2) : -0.24000                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.19                            
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) : 0.21                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.14                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.014                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.500                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 17.50                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.940                           
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) : 0.400 ; 1.500                
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 0.690 ; 2.000                
REMARK   3   SIDE-CHAIN BOND              (A**2) : 0.000 ; 2.000                
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 0.000 ; 2.500                
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 1JO2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-01.                  
REMARK 100 THE DEPOSITION ID IS D_1000013992.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 24-JUN-96                          
REMARK 200  TEMPERATURE           (KELVIN) : 293.0                              
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                             
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.54                               
REMARK 200  MONOCHROMATOR                  : GRAPHITE                           
REMARK 200  OPTICS                         : MIRRORS                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IIC                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : R-AXIS                             
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 10.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : NULL                               
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: NULL                         
REMARK 200 SOFTWARE USED: NULL                                                  
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 55.55                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, CACODYLATE, MPD,     
REMARK 280  PH 7.00, EVAPORATION, TEMPERATURE 293K                              
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -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       26.58000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       14.02500            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       14.02500            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       13.29000            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       14.02500            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       14.02500            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       39.87000            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       14.02500            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       14.02500            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       13.29000            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       14.02500            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       14.02500            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       39.87000            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       26.58000            
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 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  0.000000 -1.000000  0.000000       28.05000            
REMARK 350   BIOMT2   2 -1.000000  0.000000  0.000000       28.05000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       26.58000            
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500     DC A   5         0.09    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1JO2 A    1     6  PDB    1JO2     1JO2             1      6             
SEQRES   1 A    6   DC   G  DA  DT  DC  DG                                      
HET    DM1  A   7      38                                                       
HETNAM     DM1 DAUNOMYCIN                                                       
HETSYN     DM1 DAUNORUBICIN                                                     
FORMUL   2  DM1    C27 H29 N O10                                                
FORMUL   3  HOH   *40(H2 O)                                                     
SITE     1 AC1 12  DC A   1    G A   2   DA A   3   DT A   4                    
SITE     2 AC1 12  DC A   5   DG A   6  HOH A 102  HOH A 110                    
SITE     3 AC1 12 HOH A 111  HOH A 113  HOH A 123  HOH A 135                    
CRYST1   28.050   28.050   53.160  90.00  90.00  90.00 P 41 21 2     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      0.035651  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.035651  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.018811        0.00000