HEADER DNA 12-FEB-01 1I34 TITLE SOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TWO TITLE 2 DIAGONAL LOOPS CONNECTING GGGG TETRADS FLANKED BY G-(T-T) TRIAD AND TITLE 3 T-T-T TRIPLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*CP*AP*GP*GP*GP*TP*TP*TP*TP*GP COMPND 3 *GP*T)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DIAGONAL LOOP, DOUBLE CHAIN REVERSAL LOOP, G(SYN)-G(SYN)-G(ANTI)- KEYWDS 2 G(ANTI) TETRADS, G-(T-T) TRIAD, UNIMOLECULAR G-QUADRUPLEX, T-T-T KEYWDS 3 TRIPLE, DEOXYRIBONUCLEIC ACID, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR V.KURYAVYI,A.MAJUMDAR,A.SHALLOP,N.CHERNICHENKO,E.SKRIPKIN,R.JONES, AUTHOR 2 D.J.PATEL REVDAT 3 23-FEB-22 1I34 1 REMARK 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,E.SKRIPKIN, JRNL AUTH 2 R.JONES,D.J.PATEL JRNL TITL A DOUBLE CHAIN REVERSAL LOOP AND TWO DIAGONAL LOOPS DEFINE JRNL TITL 2 THE ARCHITECTURE OF A UNIMOLECULAR DNA QUADRUPLEX CONTAINING JRNL TITL 3 A PAIR OF STACKED G(SYN)-G(SYN)-G(ANTI)-G(ANTI) TETRADS JRNL TITL 4 FLANKED BY A 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 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 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. FOURTEEN STRUCTURES WERE REMARK 3 IDENTIFIED BASED ON THE CRITERION ACCEPTABLE COVALENT GEOMETRY, REMARK 3 LOW DISTANCE RESTRAINT VIOLATIONS AND FAVORABLE NON-BONDED REMARK 3 ENERGY. THE VARIATION IN ENERGIES WITHIN THIS SUBSET OF REMARK 3 STRUCTURES WAS 46 KCAL/MOL AND WAS SEPARATED FROM THE REMAINING REMARK 3 STRUCTURES BY A GAP OF 200 KCAL/MOL. THE TEN BEST STRUCTURES REMARK 3 FROM THIS SUBSET OF FOURTEEN 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. 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 ANGLE REMARK 3 RESTRAINTS AND HYDROGEN BONDS OF THE GGGG TETRADS WERE REMARK 3 MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO REMARK 3 RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES REMARK 3 WERE USED AS RESTRAINTS AND NON-EXCHANGEABLE PROTON DISTANCE REMARK 3 RESTRAINTS WITH THE SCALE FACTOR OF 0.1 RELATIVE TO THE REMARK 3 INTENSITY RESTRAINTS. SOFT PLANARITY RESTRAINTS MAINTAINED REMARK 3 DURING RELAXATION REFINEMENTS WERE SWITCHED OFF BEFORE THE FINAL REMARK 3 STEPS OF MINIMIZATION. THE RELAXATION PATHWAYS WERE CALCULATED REMARK 3 USING CUTOFF 4.5 ANGSTROM AND 7.91 NS ISOTROPIC CORRELATION REMARK 3 TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. 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 DEPOSITION ID IS D_1000012843. 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; 5- REMARK 210 10MM DNA (SINGLE STRANDS); 5MM REMARK 210 SODIUM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; COSY-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 II REMARK 210 2000 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 : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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,BACK- REMARK 210 CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY 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 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: 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. = -2.6 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. = 3.5 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. = 4.2 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. = 2.9 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 MODEL 1