PDB Short entry for 5WSR
HEADER    DNA                                     08-DEC-16   5WSR              
TITLE     CRYSTAL STRUCTURE OF T-HG-T PAIR CONTAINING DNA DUPLEX                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3');                    
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: UNIDENTIFIED;                                   
SOURCE   4 ORGANISM_TAXID: 32644                                                
KEYWDS    DNA DUPLEX, T-HG-T PAIR, DNA                                          
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.H.GAN,H.H.LIU                                                       
REVDAT   4   20-MAR-24 5WSR    1       LINK                                     
REVDAT   3   30-AUG-17 5WSR    1       REMARK                                   
REVDAT   2   03-MAY-17 5WSR    1       JRNL                                     
REVDAT   1   08-FEB-17 5WSR    0                                                
JRNL        AUTH   H.H.LIU,C.CAI,P.HARUEHANROENGRA,Q.Q.YAO,Y.Q.CHEN,C.YANG,     
JRNL        AUTH 2 Q.LUO,B.X.WU,J.X.LI,J.B.MA,J.SHENG,J.H.GAN                   
JRNL        TITL   FLEXIBILITY AND STABILIZATION OF HGII-MEDIATED C:T AND T:T   
JRNL        TITL 2 BASE PAIRS IN DNA DUPLEX                                     
JRNL        REF    NUCLEIC ACIDS RES.            V.  45  2910 2017              
JRNL        REFN                   ESSN 1362-4962                               
JRNL        PMID   27998930                                                     
JRNL        DOI    10.1093/NAR/GKW1296                                          
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.50 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 : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 21.57                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.370                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 95.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 3784                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.169                           
REMARK   3   R VALUE            (WORKING SET) : 0.168                           
REMARK   3   FREE R VALUE                     : 0.188                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.680                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 215                             
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 21.5710 -  1.8892    0.95     1839   102  0.1721 0.1677        
REMARK   3     2  1.8892 -  1.4996    0.95     1730   113  0.1559 0.2524        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
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)     : 0.120            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.320           
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  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      :  0.006            178                                  
REMARK   3   ANGLE     :  0.586            273                                  
REMARK   3   CHIRALITY :  0.024             31                                  
REMARK   3   PLANARITY :  0.003              8                                  
REMARK   3   DIHEDRAL  : 12.337             76                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 5WSR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-16.                  
REMARK 100 THE DEPOSITION ID IS D_1300002324.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 30-OCT-16                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRF                               
REMARK 200  BEAMLINE                       : BL19U1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.979                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS3 S 6M              
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-3000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-3000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 3784                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.0                               
REMARK 200  DATA REDUNDANCY                : 20.60                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 17.6000                            
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: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD                          
REMARK 200 SOFTWARE USED: SHELXDE                                               
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 47.41                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V MPD, VAPOR DIFFUSION, HANGING    
REMARK 280  DROP, TEMPERATURE 291K                                              
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2                        
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+1/2,X+1/2,Z+3/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
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       12.51350            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       21.26200            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       21.26200            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       18.77025            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       21.26200            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       21.26200            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        6.25675            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       21.26200            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       21.26200            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       18.77025            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       21.26200            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       21.26200            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        6.25675            
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       12.51350            
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: 1140 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 2900 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL                        
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      HOH A 240  LIES ON A SPECIAL POSITION.                          
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   O    HOH A   213     O    HOH A   242              2.18            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
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   RES CSSEQI ATM2   DEVIATION                     
REMARK 500     DC A   7   P      DC A   7   OP2    -0.111                       
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 A 252        DISTANCE =  6.43 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                              HG A 101  HG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DT A   3   O2                                                     
REMARK 620 2  DT A   3   O2  130.9                                              
REMARK 620 3  DT A   6   N3  161.4  67.4                                        
REMARK 620 4  DT A   6   N3  126.4  17.2  72.0                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              HG A 101  HG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DT A   3   N3                                                     
REMARK 620 2  DT A   3   N3  100.2                                              
REMARK 620 3  DT A   6   O4  159.5  75.1                                        
REMARK 620 4  DT A   6   O4   92.6  21.8  89.4                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue HG A 101                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5WSP   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5WSQ   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5WSS   RELATED DB: PDB                                   
DBREF  5WSR A    1     8  PDB    5WSR     5WSR             1      8             
SEQRES   1 A    8   DG  DG  DT  DC  DG  DT  DC  DC                              
HET     HG  A 101       2                                                       
HETNAM      HG MERCURY (II) ION                                                 
FORMUL   2   HG    HG 2+                                                        
FORMUL   3  HOH   *52(H2 O)                                                     
LINK         O2   DT A   3                HG  A HG A 101     7555   1555  2.02  
LINK         N3   DT A   3                HG  B HG A 101     7555   1555  2.01  
LINK         O2   DT A   3                HG  A HG A 101     1555   7555  2.02  
LINK         N3   DT A   3                HG  B HG A 101     1555   7555  2.01  
LINK         N3   DT A   6                HG  A HG A 101     1555   1555  2.03  
LINK         O4   DT A   6                HG  B HG A 101     1555   1555  2.04  
LINK         N3   DT A   6                HG  A HG A 101     7555   7555 10.77  
LINK         O4   DT A   6                HG  B HG A 101     7555   7555 10.07  
SITE     1 AC1  6  DG A   2   DT A   3   DC A   4   DG A   5                    
SITE     2 AC1  6  DT A   6   DC A   7                                          
CRYST1   42.524   42.524   25.027  90.00  90.00  90.00 P 43 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      0.023516  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.023516  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.039957        0.00000