HEADER DNA 13-OCT-99 1D6D TITLE SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED TITLE 2 BETWEEN A-T BASE PAIRS AND GGGG TETRADS; 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 TELOMERIC SOURCE 4 DNA, HUMAN IG SUPERFAMILY CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN SOURCE 5 GENE AND 16S RRNA OF HENRICA NIPONICA. KEYWDS MULTI-STRANDED DNA ARCHITECTURE, G-TETRAD, T-(A-A) TRIAD, A(SYN)- KEYWDS 2 A(ANTI) PLATFORM, ZIPPER MOTIF, BASE-SUGAR STACKING, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR V.V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL REVDAT 5 16-FEB-22 1D6D 1 REMARK 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 CONTAINING JRNL TITL 2 TRIADS SANDWICHED BETWEEN MISMATCHES 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 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 STRUCTURES REMARK 3 WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY REMARK 3 PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED REMARK 3 EXPERIMENTALLY SPECIFIED AS NOE WITH THE "SUM" AVERAGING REMARK 3 OPTION.TEN BEST STRUCTURES SELECTED ON THE BASIS OF GOOD REMARK 3 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 TEMPERATURE REMARK 3 WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE REMARK 3 CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE REMARK 3 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 TO REMARK 3 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 TO REMARK 3 RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSIY VOLUMES REMARK 3 WERE USED AS RESTRAINTS. THE RELAXATION PATHWAYS WERE CALCULATED REMARK 3 USING CUTOFF 4.5 ANGSTROM AND 7.25 NS ISOTROPIC CORRELATION REMARK 3 TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.16 A. REMARK 3 IN TWO STRUCTURES THE RESIDUES T6 AND T8 DEVIATE FROM TWO REMARK 3 CLUSTERS FORMED BY REST OF 8 STRUCTURES, AND THESE TWO REMARK 3 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 DEPOSITION ID IS D_1000009829. 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; 5- REMARK 210 10 MM DNA (SINGLE STRANDS); 5MM REMARK 210 SODIUM PHOSPHATE BUFFER; 5-10 MM REMARK 210 DNA (SINGLE STRANDS); 5MM SODIUM REMARK 210 PHOSPHATE BUFFER;SINGLE BASE REMARK 210 SUBSTITUTED FOR 8-BRDG, 8-BRDA, REMARK 210 DU, 5BRDU OR 2,6DA.; 5-10 MM DNA REMARK 210 (SINGLE STRANDS); 5MM SODIUM REMARK 210 PHOSPHATE BUFFER;SINGLE BASE REMARK 210 SUBSTITUTED FOR 8-BRDG, 8-BRDA, REMARK 210 DU, 5BRDU OR 2,6DA. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; COSY-45; REMARK 210 1H-31P COSY ON ORIGINAL AND SITE- REMARK 210 SPECIFIC SUBSTITUTED SAMPLES REMARK 210 CONTAINING 8BR-A, 8BR-G,DU,5BR- REMARK 210 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 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING, DISTANCE RESTRAINED REMARK 210 MOLECULAR DYNAMICS REFINEMENT REMARK 210 AND RELAXATION MATRIX INTENSITY REMARK 210 REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE 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 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 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: 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 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 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. = 3.5 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 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. = 4.0 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. = 3.4 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 MODEL 1