HEADER DNA 10-JUN-11 2LE6 TITLE STRUCTURE OF A DIMERIC ALL-PARALLEL-STRANDED G-QUADRUPLEX STACKED VIA TITLE 2 THE 5'-TO-5' INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC DNA KEYWDS HIV-1 INTEGRASE INHIBITION, G-QUADRUPLEX, ANTICANCER, STACKING, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.Q.DO,K.W.LIM,M.H.TEO,B.HEDDI,A.T.PHAN REVDAT 1 31-AUG-11 2LE6 0 JRNL AUTH N.Q.DO,K.W.LIM,M.H.TEO,B.HEDDI,A.T.PHAN JRNL TITL STACKING OF G-QUADRUPLEXES: NMR STRUCTURE OF A G-RICH JRNL TITL 2 OLIGONUCLEOTIDE WITH POTENTIAL ANTI-HIV AND ANTICANCER JRNL TITL 3 ACTIVITY JRNL REF NUCLEIC ACIDS RES. 2011 JRNL REFN ESSN 1362-4962 JRNL PMID 21840903 JRNL DOI 10.1093/NAR/GKR539 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10, X-PLOR_NIH REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM (AMBER), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR_NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LE6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-11. REMARK 100 THE RCSB ID CODE IS RCSB102284. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100MM K+ REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-2.0 MM DNA (5'-D(*GP*IP*GP* REMARK 210 TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1, 90% H2O/10% D2O; REMARK 210 0.5-2.0 MM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP* REMARK 210 GP*T)-3')-2, 100% D2O; 0.5-2.0 MM [U-2% 15N; U-2% 13C] DNA (5'- REMARK 210 D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-3, 90% REMARK 210 H2O/10% D2O; 0.5-2.0 MM [U-100% 2H] DNA (5'-D(*GP*IP*GP*TP*GP*GP* REMARK 210 GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-4, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C JR HMBC; 2D 1H-1H JR REMARK 210 NOESY; 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 COSY; 2D 1H-1H TOCSY; 2D 1H-13C REMARK 210 HSQC; H-D EXCHANGE; 15N-FILTERED; REMARK 210 D-LABELED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, FELIX 2007, X-PLOR_ REMARK 210 NIH 2.27 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, DISTANCE-RESTRAINED REMARK 210 MOLECULAR DYNAMICS REFINEMENT IN REMARK 210 VACUO, DISTANCE-RESTRAINED REMARK 210 MOLECULAR DYNAMICS REFINEMENT IN REMARK 210 EXPLICIT SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT B 12 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 10 DT B 12 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y8D RELATED DB: PDB REMARK 900 DIMERIC PARALLEL-STRANDED TETRAPLEX WITH 3+1 5' G-TETRAD REMARK 900 INTERFACE, SINGLE-RESIDUE CHAIN REVERSAL LOOPS AND A(GGGG) REMARK 900 PENTAD REMARK 900 RELATED ID: 17697 RELATED DB: BMRB DBREF 2LE6 A 1 16 PDB 2LE6 2LE6 1 16 DBREF 2LE6 B 1 16 PDB 2LE6 2LE6 1 16 SEQRES 1 A 16 DG DI DG DT DG DG DG DT DG DG DG DT DG SEQRES 2 A 16 DG DG DT SEQRES 1 B 16 DG DI DG DT DG DG DG DT DG DG DG DT DG SEQRES 2 B 16 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 116 0 0 0 0 0 0 6 0 0 0 4 END