HEADER    DNA                                     06-JAN-11   2L88              
TITLE     SOLUTION STRUCTURE OF ALL PARALLEL G-QUADRUPLEX FORMED BY THE ONCOGENE
TITLE    2 RET PROMOTER SEQUENCE                                                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP
COMPND   3 *GP*T)-3';                                                           
COMPND   4 CHAIN: A;                                                            
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 OTHER_DETAILS: RET ONCOGENE                                          
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;                            
SOURCE   4 ORGANISM_TAXID: 32630                                                
KEYWDS    G-QUADRUPLEX, RET, DNA                                                
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    X.TONG,C.CAO                                                          
REVDAT   5   15-MAY-24 2L88    1       REMARK                                   
REVDAT   4   14-JUN-23 2L88    1       REMARK                                   
REVDAT   3   15-FEB-23 2L88    1       SOURCE REMARK                            
REVDAT   2   28-DEC-11 2L88    1       JRNL   VERSN                             
REVDAT   1   25-MAY-11 2L88    0                                                
JRNL        AUTH   X.TONG,W.LAN,X.ZHANG,H.WU,M.LIU,C.CAO                        
JRNL        TITL   SOLUTION STRUCTURE OF ALL PARALLEL G-QUADRUPLEX FORMED BY    
JRNL        TITL 2 THE ONCOGENE RET PROMOTER SEQUENCE                           
JRNL        REF    NUCLEIC ACIDS RES.            V.  39  6753 2011              
JRNL        REFN                   ISSN 0305-1048                               
JRNL        PMID   21540209                                                     
JRNL        DOI    10.1093/NAR/GKR233                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR NIH 2.17, X-PLOR NIH 2.17                     
REMARK   3   AUTHORS     : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR     
REMARK   3                 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-   
REMARK   3                 PLOR NIH)                                            
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2L88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-11.                  
REMARK 100 THE DEPOSITION ID IS D_1000102079.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.8                                
REMARK 210  IONIC STRENGTH                 : 0.1                                
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.2-3MM POTASSIUM PHOSPHATE; 90%   
REMARK 210                                   H2O/10% D2O; 0.2-3MM POTASSIUM     
REMARK 210                                   PHOSPHATE; 100% D2O                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-1H NOESY; 2D 1H-1H TOCSY;    
REMARK 210                                   2D 1H-13C HSQC; 2D DQF-COSY        
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : INOVA                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE, SPARKY                    
REMARK 210   METHOD USED                   : DGSA-DISTANCE GEOMETRY SIMULATED   
REMARK 210                                   ANNEALING                          
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
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: MONOMERIC                         
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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
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   H22   DG A     3     H42   DC A     5              1.14            
REMARK 500   H1'   DG A    14     O6    DG A    16              1.49            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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  1  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.8 DEGREES          
REMARK 500  2  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   3.0 DEGREES          
REMARK 500  3  DG A   7   O4' -  C1' -  N9  ANGL. DEV. =   1.9 DEGREES          
REMARK 500  3  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.8 DEGREES          
REMARK 500  4  DG A   7   O4' -  C1' -  N9  ANGL. DEV. =   1.8 DEGREES          
REMARK 500  4  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.8 DEGREES          
REMARK 500  5  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.6 DEGREES          
REMARK 500  6  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.4 DEGREES          
REMARK 500  7  DG A   7   O4' -  C1' -  N9  ANGL. DEV. =   1.8 DEGREES          
REMARK 500  7  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.9 DEGREES          
REMARK 500  8  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   3.1 DEGREES          
REMARK 500  9  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.9 DEGREES          
REMARK 500 10  DG A  19   O4' -  C1' -  N9  ANGL. DEV. =   2.9 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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  1  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  2  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  3  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  4  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  5  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  6  DG A  19         0.08    SIDE CHAIN                              
REMARK 500  7  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  8  DG A  19         0.07    SIDE CHAIN                              
REMARK 500  9  DG A  19         0.07    SIDE CHAIN                              
REMARK 500 10  DG A  19         0.07    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2F8U   RELATED DB: PDB                                   
REMARK 900 SOLUTION STRUCTURE OF G-QUADRUPLEX FORMED IN THE HUMAN BCL-2         
REMARK 900 PROMOTER                                                             
REMARK 900 RELATED ID: 17397   RELATED DB: BMRB                                 
DBREF  2L88 A    1    20  PDB    2L88     2L88             1     20             
SEQRES   1 A   20   DG  DG  DG  DG  DC  DG  DG  DG  DG  DC  DG  DG  DG          
SEQRES   2 A   20   DG  DC  DG  DG  DG  DG  DT                                  
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
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      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000                         
MODEL        1