PDB Short entry for 5IYE
HEADER    DNA                                     24-MAR-16   5IYE              
TITLE     COMPARISON OF X-RAY CRYSTAL STRUCTURES OF A TETRADECAMER SEQUENCE     
TITLE    2 D(CCCGGGTACCCGGG)2 AT 1.7 RESOLUTION                                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*G)-3');  
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;                            
SOURCE   4 ORGANISM_TAXID: 32630                                                
KEYWDS    A-DNA DUPLEX, TETRAGONAL SPACE GROUP, ZINC INTERACTIONS, DNA          
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.KARTHIK,A.THIRUGNANASAMBANDAM,P.K.MANDAL,N.GAUTHAM                  
REVDAT   5   08-NOV-23 5IYE    1       REMARK                                   
REVDAT   4   30-JAN-19 5IYE    1       REMARK                                   
REVDAT   3   06-DEC-17 5IYE    1       JRNL                                     
REVDAT   2   19-APR-17 5IYE    1       JRNL                                     
REVDAT   1   29-MAR-17 5IYE    0                                                
JRNL        AUTH   S.KARTHIK,A.THIRUGNANASAMBANDAM,P.K.MANDAL,N.GAUTHAM         
JRNL        TITL   COMPARISON OF X-RAY CRYSTAL STRUCTURES OF A TETRADECAMER     
JRNL        TITL 2 SEQUENCE D(CCCGGGTACCCGGG)2 AT 1.7 ANGSTROM RESOLUTION.      
JRNL        REF    NUCLEOSIDES NUCLEOTIDES       V.  36   343 2017              
JRNL        REF  2 NUCLEIC ACIDS                                                
JRNL        REFN                   ISSN 1532-2335                               
JRNL        PMID   28387634                                                     
JRNL        DOI    10.1080/15257770.2017.1287378                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.69 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.10.1_2155                                   
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 27.79                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.450                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 98.3                           
REMARK   3   NUMBER OF REFLECTIONS             : 16056                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.191                           
REMARK   3   R VALUE            (WORKING SET) : 0.188                           
REMARK   3   FREE R VALUE                     : 0.220                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.910                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1591                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 27.7955 -  3.7641    0.95     1257   139  0.1308 0.1505        
REMARK   3     2  3.7641 -  2.9888    1.00     1335   140  0.1606 0.2175        
REMARK   3     3  2.9888 -  2.6113    1.00     1341   154  0.2458 0.2674        
REMARK   3     4  2.6113 -  2.3727    1.00     1342   142  0.2189 0.2386        
REMARK   3     5  1.7484 -  1.6938    0.87     1179   132  0.2408 0.2542        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.170            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.080           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 27.71                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 34.45                          
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  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.013            636                                  
REMARK   3   ANGLE     :  1.553            978                                  
REMARK   3   CHIRALITY :  0.078            110                                  
REMARK   3   PLANARITY :  0.010             28                                  
REMARK   3   DIHEDRAL  : 14.044            272                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : 2                                          
REMARK   3   TLS GROUP : 1                                                      
REMARK   3    SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 14 )                    
REMARK   3    ORIGIN FOR THE GROUP (A):   2.0752  14.2471  -2.5128              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:   0.2813 T22:   0.3563                                     
REMARK   3      T33:   0.3094 T12:  -0.0476                                     
REMARK   3      T13:   0.0108 T23:  -0.0532                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:  -0.7336 L22:   0.9321                                     
REMARK   3      L33:   0.8464 L12:  -1.2092                                     
REMARK   3      L13:  -0.3319 L23:  -0.8553                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:  -0.1788 S12:   0.1111 S13:  -0.0728                       
REMARK   3      S21:  -0.1690 S22:   0.4188 S23:  -0.1728                       
REMARK   3      S31:   0.1296 S32:   0.0547 S33:   0.0219                       
REMARK   3   TLS GROUP : 2                                                      
REMARK   3    SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 )                    
REMARK   3    ORIGIN FOR THE GROUP (A):   2.0613  15.0277   2.0613              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:   0.2747 T22:   0.3714                                     
REMARK   3      T33:   0.3233 T12:   0.0461                                     
REMARK   3      T13:  -0.0100 T23:  -0.0628                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:  -0.9652 L22:   0.7738                                     
REMARK   3      L33:   0.6177 L12:   1.4515                                     
REMARK   3      L13:   0.1571 L23:  -0.8753                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:  -0.1552 S12:  -0.1129 S13:   0.0909                       
REMARK   3      S21:   0.1955 S22:   0.4420 S23:  -0.0910                       
REMARK   3      S31:  -0.1736 S32:   0.0166 S33:   0.0537                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN       
REMARK   3  F_PLUS/MINUS COLUMNS                                                
REMARK   4                                                                      
REMARK   4 5IYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-16.                  
REMARK 100 THE DEPOSITION ID IS D_1000219623.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 01-JUL-13                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : BM14                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.282                              
REMARK 200  MONOCHROMATOR                  : SI(III) MONOCHROMATOR              
REMARK 200  OPTICS                         : BENT COLLIMATING MIRROR            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARMOSAIC 225 MM CCD               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS GPLV2                          
REMARK 200  DATA SCALING SOFTWARE          : NULL                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 16064                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.690                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 27.792                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.4                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : 0.04500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 21.7400                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.80                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 92.9                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.27600                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.690                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER 2.5.5                                          
REMARK 200 STARTING MODEL: 3V9D                                                 
REMARK 200                                                                      
REMARK 200 REMARK: HEXAGONAL SHAPED SINGLE LARGE CRYSTAL.                       
REMARK 200  THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.           
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 59.15                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM DNA, 50MM SODIUM CACODYLATE          
REMARK 280  BUFFER, 8MM ZNCL2, 10MM SPERMINE, 40% MPD, PH 7.0, VAPOR            
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 293K                           
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41                             
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y,X,Z+1/4                                              
REMARK 290       4555   Y,-X,Z+3/4                                              
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       44.10650            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       22.05325            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       66.15975            
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 1650 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 5230 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL                        
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     DC A   3   O4' -  C1' -  N1  ANGL. DEV. =   1.9 DEGREES          
REMARK 500     DC A   9   OP1 -  P   -  OP2 ANGL. DEV. =   9.2 DEGREES          
REMARK 500     DC A   9   O5' -  P   -  OP2 ANGL. DEV. =  -7.5 DEGREES          
REMARK 500     DC A   9   O4' -  C1' -  N1  ANGL. DEV. =   1.8 DEGREES          
REMARK 500     DC B   3   O4' -  C1' -  N1  ANGL. DEV. =   2.6 DEGREES          
REMARK 500     DT B   7   O4' -  C1' -  N1  ANGL. DEV. =   2.0 DEGREES          
REMARK 500     DA B   8   O4' -  C1' -  N9  ANGL. DEV. =   1.8 DEGREES          
REMARK 500     DC B   9   OP1 -  P   -  OP2 ANGL. DEV. =   9.5 DEGREES          
REMARK 500     DC B   9   O5' -  P   -  OP2 ANGL. DEV. =  -7.0 DEGREES          
REMARK 500     DC B   9   O4' -  C1' -  N1  ANGL. DEV. =   2.1 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                              ZN A 101  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DG A  13   N7                                                     
REMARK 620 2 HOH A 214   O    97.9                                              
REMARK 620 N                    1                                               
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5IYG   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5IYJ   RELATED DB: PDB                                   
DBREF  5IYE A    1    14  PDB    5IYE     5IYE             1     14             
DBREF  5IYE B    1    14  PDB    5IYE     5IYE             1     14             
SEQRES   1 A   14   DC  DC  DC  DG  DG  DG  DT  DA  DC  DC  DC  DG  DG          
SEQRES   2 A   14   DG                                                          
SEQRES   1 B   14   DC  DC  DC  DG  DG  DG  DT  DA  DC  DC  DC  DG  DG          
SEQRES   2 B   14   DG                                                          
HET     ZN  A 101       1                                                       
HET     ZN  B 101       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   3   ZN    2(ZN 2+)                                                     
FORMUL   5  HOH   *46(H2 O)                                                     
LINK         N7   DG A  13                ZN    ZN A 101     1555   1555  2.56  
LINK        ZN    ZN A 101                 O   HOH A 214     1555   1555  1.93  
LINK        ZN    ZN B 101                 O   HOH B 213     1555   1555  2.47  
SITE     1 AC1  2  DG A  13  HOH A 214                                          
SITE     1 AC2  4  DG B  13  HOH B 207  HOH B 210  HOH B 213                    
CRYST1   29.283   29.283   88.213  90.00  90.00  90.00 P 41          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      0.034150  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.034150  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.011336        0.00000