HEADER    DNA                                     10-MAY-06   2GYX              
TITLE     CRYSTAL STRUCTURE OF DB884- D(CGCGAATTCGCG)2 COMPLEX AT 1.86 A        
TITLE    2 RESOLUTION.                                                          
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    B-TYPE DUPLEX DNA, DOUBLE HELIX, DODECAMER, COMPOUND DB 884., DNA     
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    M.P.H.LEE,S.NEIDLE                                                    
REVDAT   5   30-AUG-23 2GYX    1       REMARK LINK                              
REVDAT   4   24-JUL-19 2GYX    1       REMARK                                   
REVDAT   3   18-OCT-17 2GYX    1       REMARK                                   
REVDAT   2   24-FEB-09 2GYX    1       VERSN                                    
REVDAT   1   22-MAY-07 2GYX    0                                                
JRNL        AUTH   M.MUNDE,M.P.H.LEE,S.NEIDLE,R.ARAFA,D.W.BOYKIN,Y.LIU,         
JRNL        AUTH 2 C.BAILLY,W.D.WILSON                                          
JRNL        TITL   INDUCED FIT CONFORMATIONAL CHANGES OF A "REVERSED AMIDINE"   
JRNL        TITL 2 HETEROCYCLE: OPTIMIZED INTERACTIONS IN A DNA MINOR GROOVE    
JRNL        TITL 3 COMPLEX.                                                     
JRNL        REF    J.AM.CHEM.SOC.                V. 129  5688 2007              
JRNL        REFN                   ISSN 0002-7863                               
JRNL        PMID   17425312                                                     
JRNL        DOI    10.1021/JA069003N                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.86 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) : 1.86                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 4.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 88.0                           
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) : 0.236                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.230                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.327                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.129                 
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 550                    
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 5430                   
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.225                  
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : 0.219                  
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : 0.310                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.102                 
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 483                    
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 4781                   
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    : 36                                            
REMARK   3   SOLVENT ATOMS      : 44                                            
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 566.00                  
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 0                       
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 2267                    
REMARK   3   NUMBER OF RESTRAINTS                     : 2584                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.006                   
REMARK   3   ANGLE DISTANCES                      (A) : 0.025                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000                   
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.012                   
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.000                   
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.005                   
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.013                   
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.000                   
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.071                   
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: NULL                                      
REMARK   4                                                                      
REMARK   4 2GYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-06.                  
REMARK 100 THE DEPOSITION ID IS D_1000037719.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 10-FEB-06                          
REMARK 200  TEMPERATURE           (KELVIN) : 105.0                              
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 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          : DENZO                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 5536                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.860                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.7                               
REMARK 200  DATA REDUNDANCY                : 2.850                              
REMARK 200  R MERGE                    (I) : 0.04300                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 35.9306                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.93                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 91.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.21400                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.310                              
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   (%): 41.36                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, MPD, DNA, COMPOUND   
REMARK 280  DB 884, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, SITTING DROP,    
REMARK 280  TEMPERATURE 293K, PH 7.00                                           
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       12.19000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       32.81350            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       20.05100            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       32.81350            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       12.19000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       20.05100            
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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500     DA A   5   O4' -  C1' -  N9  ANGL. DEV. =  -4.5 DEGREES          
REMARK 500     DT A   7   O4' -  C1' -  N1  ANGL. DEV. =  -4.5 DEGREES          
REMARK 500     DG A  10   C3' -  C2' -  C1' ANGL. DEV. =  -5.2 DEGREES          
REMARK 500     DG A  10   O4' -  C1' -  N9  ANGL. DEV. =   2.1 DEGREES          
REMARK 500     DA B  18   O4' -  C1' -  N9  ANGL. DEV. =  -4.3 DEGREES          
REMARK 500     DT B  19   O4' -  C1' -  N1  ANGL. DEV. =  -6.6 DEGREES          
REMARK 500     DC B  21   O4' -  C1' -  N1  ANGL. DEV. =  -7.1 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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  65   O                                                      
REMARK 620 2 HOH A  66   O    89.4                                              
REMARK 620 3 HOH A  67   O    89.6  89.9                                        
REMARK 620 4 HOH B  64   O    90.6 179.9  90.1                                  
REMARK 620 5 HOH B  65   O   179.8  90.4  90.4  89.6                            
REMARK 620 6 HOH B  66   O    90.4  90.3 179.8  89.6  89.6                      
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 RKA A 25                  
DBREF  2GYX A    1    12  PDB    2GYX     2GYX             1     12             
DBREF  2GYX B   13    24  PDB    2GYX     2GYX            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    RKA  A  25      35                                                       
HETNAM      MG MAGNESIUM ION                                                    
HETNAM     RKA N,N'-(1H-PYRROLE-2,5-DIYLDI-4,1-PHENYLENE)                       
HETNAM   2 RKA  DIBENZENECARBOXIMIDAMIDE                                        
FORMUL   3   MG    MG 2+                                                        
FORMUL   4  RKA    C30 H25 N5                                                   
FORMUL   5  HOH   *44(H2 O)                                                     
LINK        MG    MG A  26                 O   HOH A  65     1555   1555  2.12  
LINK        MG    MG A  26                 O   HOH A  66     1555   1555  2.13  
LINK        MG    MG A  26                 O   HOH A  67     1555   1555  2.12  
LINK        MG    MG A  26                 O   HOH B  64     1555   1555  2.13  
LINK        MG    MG A  26                 O   HOH B  65     1555   1555  2.12  
LINK        MG    MG A  26                 O   HOH B  66     1555   1555  2.12  
SITE     1 AC1  6 HOH A  65  HOH A  66  HOH A  67  HOH B  64                    
SITE     2 AC1  6 HOH B  65  HOH B  66                                          
SITE     1 AC2 12  DA A   5   DA A   6   DT A   7   DT A   8                    
SITE     2 AC2 12  DC A   9   DG A  10  HOH A  60   DA B  18                    
SITE     3 AC2 12  DT B  19   DT B  20   DC B  21   DG B  22                    
CRYST1   24.380   40.102   65.627  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      0.041017  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.024936  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.015238        0.00000