10 20 30 40 50 60 70 80 1LVS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 29-MAY-02 1LVS
TITLE THE SOLUTION STRUCTURE OF D(G4T4G3)2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: G-RICH DNA OLIGOMER
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: OLIGOMER HAS BEEN PREPARED ON SOLID STATE SOURCE 4 SUPPORT USING PHOSPHORAMIDITE CHEMISTRY.
KEYWDS G-QUARTET, NMR, CATION COORDINATION, TELOMERIC REPEAT, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.CRNUGELJ,N.V.HUD,J.PLAVEC
REVDAT 3 24-FEB-09 1LVS 1 VERSN REVDAT 2 01-APR-03 1LVS 1 JRNL REVDAT 1 24-JUL-02 1LVS 0
JRNL AUTH M.CRNUGELJ,N.V.HUD,J.PLAVEC JRNL TITL THE SOLUTION STRUCTURE OF D(G(4)T(4)G(3))(2): A JRNL TITL 2 BIMOLECULAR G-QUADRUPLEX WITH A NOVEL FOLD. JRNL REF J.MOL.BIOL. V. 320 911 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12126614 JRNL DOI 10.1016/S0022-2836(02)00569-7
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6.0 REMARK 3 AUTHORS : KOLLMAN ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 517 NOE-DERIVED DISTANCE RESTRAINTS REMARK 3 ASSOCIATED WITH THE NONEXCHANGEABLE AND EXCHANGEABLE PROTONS; REMARK 3 24 HYDROGEN-BOND RESTRAINTS; 95 TORSION ANGLE RESTRAINTS FOR REMARK 3 SUGAR MOIETIES. THIRTY 250 PS SIMULATED ANNEALING CALCULATIONS REMARK 3 AT 800 K WERE INITIALLY PERFORMED. FURTHER REFINEMENT VIA REMARK 3 SOLVATED MD SIMULATIONS (750PS, TIP3P WATER, PARTICLE MESH REMARK 3 EWALD METHOD) FOLLOWED BY ENERGY MINIMIZATION.
REMARK 4 REMARK 4 1LVS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-02. REMARK 100 THE RCSB ID CODE IS RCSB016323.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 298 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 50 MM; 50 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 5 MM DG4T4G3 PER STRAND; 90% REMARK 210 H2O, 10% D2O; 50 MM NACL; PH REMARK 210 7.2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, PE-COSY, 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1A, FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES.
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' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG A 10 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 11 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT B 16 C4 - C5 - C7 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DT B 17 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DG A 10 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DG B 14 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 DT B 16 C4 - C5 - C7 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT B 16 C6 - C5 - C7 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 17 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 DG B 20 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG B 22 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DG B 22 N3 - C2 - N2 ANGL. DEV. = -6.1 DEGREES REMARK 500 3 DG A 1 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 DG A 3 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT A 5 C4 - C5 - C7 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DT A 5 C6 - C5 - C7 ANGL. DEV. = -6.7 DEGREES REMARK 500 3 DT A 6 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 8 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 237 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DT A 5 0.08 SIDE_CHAIN REMARK 500 1 DT A 7 0.09 SIDE_CHAIN REMARK 500 1 DT B 17 0.08 SIDE_CHAIN REMARK 500 2 DT A 5 0.08 SIDE_CHAIN REMARK 500 2 DT A 8 0.08 SIDE_CHAIN REMARK 500 2 DG A 9 0.10 SIDE_CHAIN REMARK 500 2 DG A 11 0.07 SIDE_CHAIN REMARK 500 2 DG B 12 0.08 SIDE_CHAIN REMARK 500 2 DG B 13 0.07 SIDE_CHAIN REMARK 500 2 DT B 17 0.09 SIDE_CHAIN REMARK 500 3 DG A 3 0.05 SIDE_CHAIN REMARK 500 3 DT A 7 0.08 SIDE_CHAIN REMARK 500 3 DG A 9 0.07 SIDE_CHAIN REMARK 500 3 DG B 12 0.06 SIDE_CHAIN REMARK 500 4 DT A 5 0.06 SIDE_CHAIN REMARK 500 4 DT B 16 0.07 SIDE_CHAIN REMARK 500 4 DT B 17 0.09 SIDE_CHAIN REMARK 500 5 DT A 5 0.09 SIDE_CHAIN REMARK 500 5 DT A 7 0.07 SIDE_CHAIN REMARK 500 5 DG A 9 0.05 SIDE_CHAIN REMARK 500 5 DG A 11 0.06 SIDE_CHAIN REMARK 500 5 DG B 12 0.05 SIDE_CHAIN REMARK 500 5 DT B 19 0.06 SIDE_CHAIN REMARK 500 6 DT A 7 0.08 SIDE_CHAIN REMARK 500 6 DG A 9 0.06 SIDE_CHAIN REMARK 500 6 DG B 12 0.05 SIDE_CHAIN REMARK 500 6 DT B 17 0.07 SIDE_CHAIN REMARK 500 7 DT A 5 0.07 SIDE_CHAIN REMARK 500 7 DT A 7 0.09 SIDE_CHAIN REMARK 500 8 DT A 7 0.17 SIDE_CHAIN REMARK 500 9 DT B 17 0.07 SIDE_CHAIN REMARK 500 10 DT A 5 0.06 SIDE_CHAIN REMARK 500 10 DG A 9 0.06 SIDE_CHAIN REMARK 500 10 DG B 12 0.08 SIDE_CHAIN REMARK 500 10 DT B 17 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1LVS A 1 11 PDB 1LVS 1LVS 1 11 DBREF 1LVS B 12 22 PDB 1LVS 1LVS 12 22
SEQRES 1 A 11 DG DG DG DG DT DT DT DT DG DG DG SEQRES 1 B 11 DG DG DG DG DT DT DT DT DG 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