HEADER    DNA                                     14-SEP-05   2B0K              
TITLE     CRYSTAL STRUCTURE OF THE DB921-D(CGCGAATTCGCG)2 COMPLEX.              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3';              
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: AT-RICH REGION IN THE GENOME OF ORGANISMS.            
KEYWDS    NUCLEIC ACIDS, DNA, DOUBLE HELIX, MINOR GROOVE, DNA MINOR GROOVE      
KEYWDS   2 BINDER, DNA MINOR GROOVE-LIGAND COMPLEX, DB921, A2T2, DICKERSON AND  
KEYWDS   3 DREW DNA, CRYSTAL STRUCTURE OF B-DNA, DNA-DRUG COMPLEX, MAGNESIUM-   
KEYWDS   4 WATER COMPLEX, HYDRATED MAGNESIUM, DNA HYDRATION.                    
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Y.MIAO,M.P.LEE,G.N.PARKINSON,A.BATISTA-PARRA,M.A.ISMAIL,S.NEIDLE,     
AUTHOR   2 D.W.BOYKIN,W.D.WILSON                                                
REVDAT   5   23-AUG-23 2B0K    1       REMARK LINK                              
REVDAT   4   24-JUL-19 2B0K    1       REMARK                                   
REVDAT   3   24-FEB-09 2B0K    1       VERSN                                    
REVDAT   2   13-DEC-05 2B0K    1       AUTHOR                                   
REVDAT   1   22-NOV-05 2B0K    0                                                
JRNL        AUTH   Y.MIAO,M.P.LEE,G.N.PARKINSON,A.BATISTA-PARRA,M.A.ISMAIL,     
JRNL        AUTH 2 S.NEIDLE,D.W.BOYKIN,W.D.WILSON                               
JRNL        TITL   OUT-OF-SHAPE DNA MINOR GROOVE BINDERS: INDUCED FIT           
JRNL        TITL 2 INTERACTIONS OF HETEROCYCLIC DICATIONS WITH THE DNA MINOR    
JRNL        TITL 3 GROOVE.                                                      
JRNL        REF    BIOCHEMISTRY                  V.  44 14701 2005              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   16274217                                                     
JRNL        DOI    10.1021/BI051791Q                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.64 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : SHELXL-97                                            
REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 87.2                           
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM                         
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.231                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.229                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.300                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.840                  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 784                    
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 7968                   
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.217                  
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : 0.214                  
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : 0.285                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.840                  
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 683                    
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 6942                   
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 0                                             
REMARK   3   NUCLEIC ACID ATOMS : 486                                           
REMARK   3   HETEROGEN ATOMS    : 28                                            
REMARK   3   SOLVENT ATOMS      : 82                                            
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 596.00                  
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 0                       
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 2399                    
REMARK   3   NUMBER OF RESTRAINTS                     : 2543                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.004                   
REMARK   3   ANGLE DISTANCES                      (A) : 0.019                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000                   
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.009                   
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.000                   
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.037                   
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.026                   
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.000                   
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.067                   
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : 0.000                   
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228        
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER                        
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES   
REMARK   3  PROCEDURE. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN,     
REMARK   3  MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56                           
REMARK   4                                                                      
REMARK   4 2B0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-05.                  
REMARK 100 THE DEPOSITION ID IS D_1000034524.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 05-MAY-05                          
REMARK 200  TEMPERATURE           (KELVIN) : 105.0                              
REMARK 200  PH                             : 6.50                               
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 RU200                       
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.54178                            
REMARK 200  MONOCHROMATOR                  : NI FILTER                          
REMARK 200  OPTICS                         : OSMIC FOCUSING MIRROR SYSTEM       
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   : 8055                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.640                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -2.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.6                               
REMARK 200  DATA REDUNDANCY                : 3.160                              
REMARK 200  R MERGE                    (I) : 0.05600                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 36.1900                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.70                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.19700                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 6.430                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: CNS                                                   
REMARK 200 STARTING MODEL: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 54.27                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, DNA, COMPOUND        
REMARK 280  DB921, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING      
REMARK 280  DROP, TEMPERATURE 293.0K, PH 6.50                                   
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       12.14400            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       32.99450            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       20.03400            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       32.99450            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       12.14400            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       20.03400            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC                           
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 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                              MG A  26  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HOH A 104   O                                                      
REMARK 620 2 HOH A 105   O    90.0                                              
REMARK 620 3 HOH A 108   O    90.0  90.0                                        
REMARK 620 4 HOH B 103   O    90.0 180.0  90.0                                  
REMARK 620 5 HOH B 106   O   179.9  90.0  89.9  90.0                            
REMARK 620 6 HOH B 107   O    90.0  90.0 179.9  90.0  90.0                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 26                   
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D2A A 25                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: GDL009   RELATED DB: NDB                                 
REMARK 900 DNA PART OF NDB ENTRY GDL009                                         
REMARK 900 RELATED ID: 2DBE   RELATED DB: PDB                                   
REMARK 900 DNA PART OF PDB ENTRY 2DBE                                           
DBREF  2B0K A    1    12  PDB    2B0K     2B0K             1     12             
DBREF  2B0K B   13    24  PDB    2B0K     2B0K            13     24             
SEQRES   1 A   12   DC  DG  DC  DG  DA  DA  DT  DT  DC  DG  DC  DG              
SEQRES   1 B   12   DC  DG  DC  DG  DA  DA  DT  DT  DC  DG  DC  DG              
HET     MG  A  26       1                                                       
HET    D2A  A  25      27                                                       
HETNAM      MG MAGNESIUM ION                                                    
HETNAM     D2A 2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE           
HETSYN     D2A DB921                                                            
FORMUL   3   MG    MG 2+                                                        
FORMUL   4  D2A    C21 H18 N6                                                   
FORMUL   5  HOH   *82(H2 O)                                                     
LINK        MG    MG A  26                 O   HOH A 104     1555   1555  2.13  
LINK        MG    MG A  26                 O   HOH A 105     1555   1555  2.13  
LINK        MG    MG A  26                 O   HOH A 108     1555   1555  2.13  
LINK        MG    MG A  26                 O   HOH B 103     1555   1555  2.12  
LINK        MG    MG A  26                 O   HOH B 106     1555   1555  2.13  
LINK        MG    MG A  26                 O   HOH B 107     1555   1555  2.13  
SITE     1 AC1  6 HOH A 104  HOH A 105  HOH A 108  HOH B 103                    
SITE     2 AC1  6 HOH B 106  HOH B 107                                          
SITE     1 AC2  8  DA A   6   DT A   7   DT A   8   DC A   9                    
SITE     2 AC2  8  DA B  18   DT B  19   DT B  20   DC B  21                    
CRYST1   24.288   40.068   65.989  90.00  90.00  90.00 P 21 21 21    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      0.041173  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.024958  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.015154        0.00000