HEADER DNA 13-OCT-99 1D6D TITLE SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS TITLE 2 INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; TITLE 3 NMR, 8 STRUCT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMAN SOURCE 4 TELOMERIC DNA, HUMAN IG SUPERFAMILY CYTOTOXIC T-LYMPHOCYTE- SOURCE 5 ASSOCIATED PROTEIN GENE AND 16S RRNA OF HENRICA NIPONICA. KEYWDS MULTI-STRANDED DNA ARCHITECTURE, G-TETRAD, T-(A-A) TRIAD, KEYWDS 2 A(SYN)-A(ANTI) PLATFORM, ZIPPER MOTIF, BASE-SUGAR STACKING EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR V.V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL REVDAT 4 24-FEB-09 1D6D 1 VERSN REVDAT 3 01-APR-03 1D6D 1 JRNL REVDAT 2 03-FEB-00 1D6D 1 JRNL REVDAT 1 17-JAN-00 1D6D 0 JRNL AUTH V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL JRNL TITL A DIAMOND-SHAPED ZIPPER-LIKE DNA ARCHITECTURE JRNL TITL 2 CONTAINING TRIADS SANDWICHED BETWEEN MISMATCHES JRNL TITL 3 AND TETRADS. JRNL REF J.MOL.BIOL. V. 295 455 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10623538 JRNL DOI 10.1006/JMBI.1999.3345 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : A.BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 100 INITIAL DNA REMARK 3 STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE REMARK 3 GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS REMARK 3 OBTAINED EXPERIMENTALLY SPECIFIED AS NOE WITH THE "SUM" REMARK 3 AVERAGING OPTION.TEN BEST STRUCTURES SELECTED ON THE BASIS OF REMARK 3 GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND REMARK 3 FAVOURABLE NON-BONDED ENERGY WERE FURTHER OPTIMIZED WITH REMARK 3 RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND REMARK 3 RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS REMARK 3 FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE REMARK 3 TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS REMARK 3 THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN REMARK 3 THE PROPORTION 1: 4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, REMARK 3 NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE REMARK 3 THEN SLOWLY COOLED TO 300K IN 2.8 PS AND EQUILIBRATED AT 300K REMARK 3 FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST REMARK 3 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED REMARK 3 TO 3000 STEPS OF MINIMIZATION. THE HYDROGEN BONDS OF THE GGGG REMARK 3 TETRADS, AND NON- CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE REMARK 3 MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED REMARK 3 TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSIY REMARK 3 VOLUMES WERE USED AS RESTRAINTS. THE RELAXATION PATHWAYS WERE REMARK 3 CALCULATED USING CUTOFF 4.5 ANGSTROM AND 7.25 NS ISOTROPIC REMARK 3 CORRELATION TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. REMARK 3 VALUE OF 1.16 A. IN TWO STRUCTURES THE RESIDUES T6 AND T8 REMARK 3 DEVIATE FROM TWO CLUSTERS FORMED BY REST OF 8 STRUCTURES, AND REMARK 3 THESE TWO STRUCTURES WERE OMITTED FROM DEPOSITION. REMARK 4 REMARK 4 1D6D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-99. REMARK 100 THE RCSB ID CODE IS RCSB009829. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5-10 MM DNA (SINGLE STRANDS); REMARK 210 5MM SODIUM PHOSPHATE BUFFER; REMARK 210 5-10 MM DNA (SINGLE STRANDS); REMARK 210 5MM SODIUM PHOSPHATE BUFFER; REMARK 210 5-10 MM DNA (SINGLE STRANDS); REMARK 210 5MM SODIUM PHOSPHATE BUFFER; REMARK 210 SINGLE BASE SUBSTITUTED FOR 8- REMARK 210 BRDG, 8-BRDA, DU, 5BRDU OR 2, REMARK 210 6DA.; 5-10 MM DNA (SINGLE REMARK 210 STRANDS); 5MM SODIUM PHOSPHATE REMARK 210 BUFFER;SINGLE BASE SUBSTITUTED REMARK 210 FOR 8-BRDG, 8-BRDA, DU, 5BRDU REMARK 210 OR 2,6DA. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, DQF-COSY, COSY- REMARK 210 45, 1H-31P COSY ON ORIGINAL REMARK 210 AND SITE-SPECIFIC SUBSTITUTED REMARK 210 SAMPLES CONTAINING 8BR-A, 8BR- REMARK 210 G,DU,5BR-DU,2,6-DA ANALOGS. REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5.0, FELIX 97.0, X-PLOR REMARK 210 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND REMARK 210 SIMULATED ANNEALING, DISTANCE REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REFINEMENT AND RELAXATION REMARK 210 MATRIX INTENSITY REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 STRUCTURES WITH FAVORABLE NON- REMARK 210 BOND ENERGY, STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 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 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 1 DA A 10 C5' DA A 10 C4' 0.045 REMARK 500 1 DA B 10 C5' DA B 10 C4' 0.045 REMARK 500 2 DA A 10 C5' DA A 10 C4' 0.048 REMARK 500 2 DA B 10 C5' DA B 10 C4' 0.048 REMARK 500 3 DA A 10 C5' DA A 10 C4' 0.042 REMARK 500 4 DA A 10 C5' DA A 10 C4' 0.045 REMARK 500 4 DA B 10 C5' DA B 10 C4' 0.046 REMARK 500 5 DA A 10 C5' DA A 10 C4' 0.050 REMARK 500 5 DA B 10 C5' DA B 10 C4' 0.050 REMARK 500 6 DA A 10 C5' DA A 10 C4' 0.042 REMARK 500 6 DA B 10 C5' DA B 10 C4' 0.042 REMARK 500 8 DA A 10 C5' DA A 10 C4' 0.054 REMARK 500 8 DA B 10 C5' DA B 10 C4' 0.054 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DA B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA B 1 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA B 2 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG B 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG B 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA B 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA B 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA B 10 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 11 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 386 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D6D A 1 12 PDB 1D6D 1D6D 1 12 DBREF 1D6D B 1 12 PDB 1D6D 1D6D 1 12 SEQRES 1 A 12 DA DA DG DG DT DT DT DT DA DA DG DG SEQRES 1 B 12 DA DA DG DG DT DT DT DT DA DA DG DG 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 201 0 0 0 0 0 0 6 0 0 0 2 END