PDB Short entry for 313D
HEADER    DNA                                     04-FEB-97   313D              
TITLE     Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE                   
TITLE    2 HOOGSTEEN BASE PAIR                                                  
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*GP*(5CM)P*GP*CP*GP*CP*G)-3');                   
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    Z-DNA, DOUBLE HELIX, MODIFIED, OVERHANGING BASE, FLIPPED-             
KEYWDS   2 OUT BASE                                                             
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    B.H.M.MOOERS,B.F.EICHMAN,P.S.HO                                       
REVDAT   3   24-FEB-09 313D    1       VERSN                                    
REVDAT   2   01-APR-03 313D    1       JRNL                                     
REVDAT   1   05-AUG-97 313D    0                                                
JRNL        AUTH   B.H.MOOERS,B.F.EICHMAN,P.S.HO                                
JRNL        TITL   THE STRUCTURES AND RELATIVE STABILITIES OF D(G X             
JRNL        TITL 2 G) REVERSE HOOGSTEEN, D(G X T) REVERSE WOBBLE, AND           
JRNL        TITL 3 D(G X C) REVERSE WATSON-CRICK BASE-PAIRS IN DNA              
JRNL        TITL 4 CRYSTALS.                                                    
JRNL        REF    J.MOL.BIOL.                   V. 269   796 1997              
JRNL        REFN                   ISSN 0022-2836                               
JRNL        PMID   9223642                                                      
JRNL        DOI    10.1006/JMBI.1997.1100                                       
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.68 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) : 1.68                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 3.000                          
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             : 3538                           
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) : 0.207                           
REMARK   3   FREE R VALUE                     : 0.287                           
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       : 284                                     
REMARK   3   HETEROGEN ATOMS          : 16                                      
REMARK   3   SOLVENT ATOMS            : 49                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 15.90                          
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) : 0.20                            
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) : 0.007                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.48                            
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  : PAR_NDB.DNA                                    
REMARK   3  PARAMETER FILE  2  : PAR_NDB_HIGH.DNA                               
REMARK   3  PARAMETER FILE  3  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : TOP_NDB.DNA                                    
REMARK   3  TOPOLOGY FILE  2   : NULL                                           
REMARK   3  TOPOLOGY FILE  3   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 313D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 01-MAY-96                          
REMARK 200  TEMPERATURE           (KELVIN) : 293.00                             
REMARK 200  PH                             : 7.00                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
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) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : AREA DETECTOR                      
REMARK 200  DETECTOR MANUFACTURER          : SIEMENS HI-STAR                    
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : SAINT                              
REMARK 200  DATA SCALING SOFTWARE          : SAINT                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 5324                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.680                              
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL                               
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 84.5                               
REMARK 200  DATA REDUNDANCY                : 2.500                              
REMARK 200  R MERGE                    (I) : 0.08600                            
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: MOLECULAR REPLACEMENT        
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   (%): NULL                                      
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION, SITTING        
REMARK 280  DROP                                                                
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       10.17000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       25.96500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       14.81000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       25.96500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       10.17000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       14.81000            
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     DG B   8   C3' -  C2' -  C1' ANGL. DEV. =  -5.2 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 525                                                                      
REMARK 525 SOLVENT                                                              
REMARK 525                                                                      
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
REMARK 525 NUMBER; I=INSERTION CODE):                                           
REMARK 525                                                                      
REMARK 525  M RES CSSEQI                                                        
REMARK 525    HOH B  19        DISTANCE =  5.20 ANGSTROMS                       
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  16  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HOH A  66   O                                                      
REMARK 620 2 HOH A  71   O    87.4                                              
REMARK 620 3 HOH A  68   O    60.3  98.1                                        
REMARK 620 4 HOH A  70   O    75.2 159.8  82.3                                  
REMARK 620 5 HOH A  69   O   108.5  95.3 162.0  81.0                            
REMARK 620 6 HOH A  67   O   160.7 101.1 101.0  98.6  88.2                      
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 16                   
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 15                  
DBREF  313D A    1     7  PDB    313D     313D             1      7             
DBREF  313D B    8    14  PDB    313D     313D             8     14             
SEQRES   1 A    7   DG 5CM  DG  DC  DG  DC  DG                                  
SEQRES   1 B    7   DG 5CM  DG  DC  DG  DC  DG                                  
MODRES 313D 5CM A    2   DC                                                     
MODRES 313D 5CM B    9   DC                                                     
HET    5CM  A   2      20                                                       
HET    5CM  B   9      20                                                       
HET     MG  A  16       1                                                       
HET    NCO  A  15       7                                                       
HETNAM     5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE                      
HETNAM      MG MAGNESIUM ION                                                    
HETNAM     NCO COBALT HEXAMMINE(III)                                            
FORMUL   1  5CM    2(C10 H16 N3 O7 P)                                           
FORMUL   3   MG    MG 2+                                                        
FORMUL   4  NCO    CO H18 N6 3+                                                 
FORMUL   5  HOH   *55(H2 O)                                                     
LINK        MG    MG A  16                 O   HOH A  66     1555   1555  2.18  
LINK        MG    MG A  16                 O   HOH A  71     1555   1555  2.10  
LINK        MG    MG A  16                 O   HOH A  68     1555   1555  2.58  
LINK        MG    MG A  16                 O   HOH A  70     1555   1555  1.97  
LINK        MG    MG A  16                 O   HOH A  69     1555   1555  2.10  
LINK        MG    MG A  16                 O   HOH A  67     1555   1555  2.30  
LINK         O3'  DG A   1                 P   5CM A   2     1555   1555  1.60  
LINK         O3' 5CM A   2                 P    DG A   3     1555   1555  1.61  
LINK         O3'  DG B   8                 P   5CM B   9     1555   1555  1.60  
LINK         O3' 5CM B   9                 P    DG B  10     1555   1555  1.61  
SITE     1 AC1  7 HOH A  66  HOH A  67  HOH A  68  HOH A  69                    
SITE     2 AC1  7 HOH A  70  HOH A  71   DG B  14                               
SITE     1 AC2  6  DC A   4   DG A   5  HOH A  44  HOH A  61                    
SITE     2 AC2  6  DG B  14  HOH B  63                                          
CRYST1   20.340   29.620   51.930  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      0.049164  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.033761  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.019257        0.00000