HEADER DNA 25-FEB-98 1A6H TITLE DNA QUADRUPLEX CONTAINING GCGC TETRAD, NMR, 4 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(GP*CP*GP*GP*TP*TP*TP*GP*CP*GP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, DNA QUADRUPLEX, FRAGILE X SYNDROME, D(CGG) KEYWDS 2 TRIPLET REPEAT, GCGC TETRADS, DNA EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR A.KETTANI,R.A.KUMAR,D.J.PATEL REVDAT 5 22-MAY-24 1A6H 1 REMARK REVDAT 4 16-FEB-22 1A6H 1 REMARK REVDAT 3 19-MAY-09 1A6H 1 REMARK REVDAT 2 24-FEB-09 1A6H 1 VERSN REVDAT 1 17-JUN-98 1A6H 0 SPRSDE 17-JUN-98 1A6H 228D JRNL AUTH A.KETTANI,R.A.KUMAR,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF A DNA QUADRUPLEX CONTAINING THE JRNL TITL 2 FRAGILE X SYNDROME TRIPLET REPEAT. JRNL REF J.MOL.BIOL. V. 254 638 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7500339 JRNL DOI 10.1006/JMBI.1995.0644 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A SET OF FOUR STRUCTURES WERE OBTAINED REMARK 3 USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED REMARK 3 BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER- REMARK 3 PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE REMARK 3 NMR DATA. THE FOUR DISTANCE-REFINED STRUCTURES WERE REFINED REMARK 3 FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED REMARK 3 MOLECULAR DYNAMICS. ALL CALCULATIONS WERE CARRIED OUT USING THE REMARK 3 X-PLOR PROGRAM. THE FINAL FOUR STRUCTURES WERE OBTAINED BY REMARK 3 CONJUGATE GRADIENT MINIMIZATION OF THE STRUCTURES OBTAINED BY REMARK 3 RELAXATION MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR REMARK 3 DYNAMICS. THE UNWEIGHTED R(1/6) VALUE WAS USED TO MONITOR THE REMARK 3 REFINEMENT. THE R(1/6)-FACTOR IS DEFINED: R(1/6) = SUM{|I(OBS)^ REMARK 3 (1/6) - K*I(CALC)^(1/6)|} / SUM{I(OBS)^(1/6)}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