HEADER DNA 12-FEB-01 1I34 TITLE SOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TITLE 2 TWO DIAGONAL LOOPS CONNECTING GGGG TETRADS FLANKED BY G-(T- TITLE 3 T) TRIAD AND T-T-T TRIPLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*GP*GP*TP*TP*TP*TP*GP*GP*CP*AP*GP*GP*GP*TP*TP*TP*TP*GP*GP COMPND 4 *T)-3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DIAGONAL LOOP, DOUBLE CHAIN REVERSAL LOOP, G(SYN)-G(SYN)- KEYWDS 2 G(ANTI)-G(ANTI) TETRADS, G-(T-T) TRIAD, UNIMOLECULAR G- KEYWDS 3 QUADRUPLEX, T-T-T TRIPLE, DEOXYRIBONUCLEIC ACID, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR V.KURYAVYI,A.MAJUMDAR,A.SHALLOP,N.CHERNICHENKO,E.SKRIPKIN, AUTHOR 2 R.JONES,D.J.PATEL REVDAT 2 24-FEB-09 1I34 1 VERSN REVDAT 1 27-JUN-01 1I34 0 JRNL AUTH V.KURYAVYI,A.MAJUMDAR,A.SHALLOP,N.CHERNICHENKO, JRNL AUTH 2 E.SKRIPKIN,R.JONES,D.J.PATEL JRNL TITL A DOUBLE CHAIN REVERSAL LOOP AND TWO DIAGONAL JRNL TITL 2 LOOPS DEFINE THE ARCHITECTURE OF A UNIMOLECULAR JRNL TITL 3 DNA QUADRUPLEX CONTAINING A PAIR OF STACKED JRNL TITL 4 G(SYN)-G(SYN)-G(ANTI)-G(ANTI) TETRADS FLANKED BY A JRNL TITL 5 G-(T-T) TRIAD AND A T-T-T TRIPLE. JRNL REF J.MOL.BIOL. V. 310 181 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11419945 JRNL DOI 10.1006/JMBI.2001.4759 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER, A.T. ET AL. 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. FOURTEEN STRUCTURES REMARK 3 WERE IDENTIFIED BASED ON THE CRITERION ACCEPTABLE COVALENT REMARK 3 GEOMETRY, LOW DISTANCE RESTRAINT VIOLATIONS AND FAVORABLE NON- REMARK 3 BONDED ENERGY. THE VARIATION IN ENERGIES WITHIN THIS SUBSET OF REMARK 3 STRUCTURES WAS 46 KCAL/MOL AND WAS SEPARATED FROM THE REMARK 3 REMAINING STRUCTURES BY A GAP OF 200 KCAL/MOL. THE TEN BEST REMARK 3 STRUCTURES FROM THIS SUBSET OF FOURTEEN WERE FURTHER OPTIMIZED REMARK 3 WITH 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. SOFT PLANARITY RESTRAINTS WERE SWITCHED OFF BEFORE REMARK 3 THE EQUILIBRATION STAGE.THE COORDINATES SAVED EVERY 0.5 PS REMARK 3 DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE REMARK 3 WAS SUBJECTED TO 3000 STEPS OF MINIMIZATION. THE DIHEDRAL REMARK 3 ANGLE RESTRAINTS AND HYDROGEN BONDS OF THE GGGG TETRADS WERE REMARK 3 MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED REMARK 3 TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY REMARK 3 VOLUMES WERE USED AS RESTRAINTS AND NON-EXCHANGEABLE PROTON REMARK 3 DISTANCE RESTRAINTS WITH THE SCALE FACTOR OF 0.1 RELATIVE TO REMARK 3 THE INTENSITY RESTRAINTS. SOFT PLANARITY RESTRAINTS MAINTAINED REMARK 3 DURING RELAXATION REFINEMENTS WERE SWITCHED OFF BEFORE THE REMARK 3 FINAL STEPS OF MINIMIZATION. THE RELAXATION PATHWAYS WERE REMARK 3 CALCULATED USING CUTOFF 4.5 ANGSTROM AND 7.91 NS ISOTROPIC REMARK 3 CORRELATION TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. REMARK 3 VALUE OF 1.07 A. REMARK 4 REMARK 4 1I34 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-01. REMARK 100 THE RCSB ID CODE IS RCSB012843. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278.00 REMARK 210 PH : 6.80 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 5-10MM DNA (SINGLE STRANDS); REMARK 210 5MM SODIUM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, DQF-COSY, COSY- REMARK 210 45 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 6.0, FELIX 2000, INSIGHT REMARK 210 II 2000 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 : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND REMARK 210 ENERGY,STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 BACK-CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 REMARK 210 REMARK 210 REMARK: SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A,8BR- REMARK 210 G,DU,5BR-DU, 2,6A, I, 5ME-C ANALOGS AND SITE-SPECIFIC OR REMARK 210 UNIFORMLY 13C AND 15N LABELED SAMPLES HAVE BEEN USED 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 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 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.0 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. = 3.4 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 13 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 19 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 19 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 378 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1I34 A 1 20 PDB 1I34 1I34 1 20 SEQRES 1 A 20 DG DG DT DT DT DT DG DG DC DA DG DG DG SEQRES 2 A 20 DT DT DT DT 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 165 0 0 0 0 0 0 6 0 0 0 2 END