PDB Short entry for 253D
HEADER    DNA                                     20-MAR-96   253D              
TITLE     CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL      
TITLE    2 D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE                   
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3');                 
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    B-DNA, DOUBLE HELIX, BASE TRIPLET, DNA                                
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    B.H.M.MOOERS,P.S.HO                                                   
REVDAT   3   14-FEB-24 253D    1       REMARK LINK                              
REVDAT   2   24-FEB-09 253D    1       VERSN                                    
REVDAT   1   15-APR-96 253D    0                                                
JRNL        AUTH   B.H.M.MOOERS,P.S.HO                                          
JRNL        TITL   CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A   
JRNL        TITL 2 NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE     
JRNL        REF    TO BE PUBLISHED                            1996              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.20 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR                                               
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 1.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL                           
REMARK   3   NUMBER OF REFLECTIONS             : 920                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : NULL                            
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            
REMARK   3   R VALUE            (WORKING SET) : 0.193                           
REMARK   3   FREE R VALUE                     : 0.214                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL                         
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : NULL                         
REMARK   3   BIN FREE R VALUE                    : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL                         
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 0                                       
REMARK   3   NUCLEIC ACID ATOMS       : 183                                     
REMARK   3   HETEROGEN ATOMS          : 1                                       
REMARK   3   SOLVENT ATOMS            : 29                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
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) : 0.27                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.012                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.620                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
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  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 253D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB.                                
REMARK 100 THE DEPOSITION ID IS D_1000177658.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 20-AUG-95                          
REMARK 200  TEMPERATURE           (KELVIN) : NULL                               
REMARK 200  PH                             : 6.00                               
REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : SEALED TUBE                        
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : DIFFRACTOMETER                     
REMARK 200  DETECTOR MANUFACTURER          : SIEMENS P4                         
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XSCANS                             
REMARK 200  DATA SCALING SOFTWARE          : NULL                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 1126                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.200                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 32.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 76.4                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : 0.04200                            
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: NULL                                           
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   (%): 45.76                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00, VAPOR DIFFUSION, HANGING DROP   
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2                        
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   -Y+1/2,X+1/2,Z+1/2                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/2                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/2                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/2                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-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  0.000000 -1.000000  0.000000       19.45750            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       19.45750            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       16.51300            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       19.45750            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       19.45750            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       16.51300            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       19.45750            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       19.45750            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       16.51300            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       19.45750            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       19.45750            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       16.51300            
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        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                                     
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        0.00000            
REMARK 350   BIOMT2   2  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375 MG    MG A  10  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A  13  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A  28  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A  36  LIES ON A SPECIAL POSITION.                          
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     DG A   1         0.10    SIDE CHAIN                              
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  10  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DG A   9   OP1                                                    
REMARK 620 2 HOH A  38   O    90.6                                              
REMARK 620 3 HOH A  39   O    76.3  83.4                                        
REMARK 620 N                    1     2                                         
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 10                   
DBREF  253D A    1     9  PDB    253D     253D             1      9             
SEQRES   1 A    9   DG  DC  DG  DT  DA  DC  DG  DC  DG                          
HET     MG  A  10       1                                                       
HETNAM      MG MAGNESIUM ION                                                    
FORMUL   2   MG    MG 2+                                                        
FORMUL   3  HOH   *29(H2 O)                                                     
LINK         OP1  DG A   9                MG    MG A  10     1555   1555  2.33  
LINK        MG    MG A  10                 O   HOH A  38     1555   1555  2.15  
LINK        MG    MG A  10                 O   HOH A  39     1555   1555  2.18  
SITE     1 AC1  3  DG A   9  HOH A  38  HOH A  39                               
CRYST1   38.915   38.915   33.026  90.00  90.00  90.00 P 42 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      0.025690  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.025690  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.030280        0.00000