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- PDB-1d6d: SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED B... -

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Basic information

Entry
Database: PDB / ID: 1d6d
TitleSOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.
Components5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3'
KeywordsDNA / MULTI-STRANDED DNA ARCHITECTURE / G-TETRAD / T-(A-A) TRIAD / A(SYN)-A(ANTI) PLATFORM / ZIPPER MOTIF / BASE-SUGAR STACKING
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
AuthorsKuryavyi, V.V. / Kettani, A. / Wang, W. / Jones, R. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: A diamond-shaped zipper-like DNA architecture containing triads sandwiched between mismatches and tetrads.
Authors: Kuryavyi, V. / Kettani, A. / Wang, W. / Jones, R. / Patel, D.J.
History
DepositionOct 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3'
B: 5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,4832
Polymers7,4832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 100BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #3fewest violations,lowest energy

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Components

#1: DNA chain 5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3'


Mass: 3741.464 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN HUMAN TELOMERIC DNA, HUMAN IG SUPERFAMILY CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN GENE AND 16S RRNA OF HENRICA NIPONICA.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141COSY-45
1511H-31P COSY ON ORIGINAL AND SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A, 8BR-G,DU,5BR-DU,2,6-DA ANALOGS.

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Sample preparation

Details
Solution-IDContents
15-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER
25-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER
35-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER;SINGLE BASE SUBSTITUTED FOR 8-BRDG, 8-BRDA, DU, 5BRDU OR 2,6DA.
45-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER;SINGLE BASE SUBSTITUTED FOR 8-BRDG, 8-BRDA, DU, 5BRDU OR 2,6DA.
Sample conditionsIonic strength: 150mM NACL / pH: 6.9 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VARIAN UNITY INOVA / Manufacturer: Varian / Model: VARIAN UNITY INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1A.BRUNGERrefinement
VNMR5VARIANcollection
Felix97BIOSYMdata analysis
X-PLOR3.1A.BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
Software ordinal: 1
Details: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED EXPERIMENTALLY SPECIFIED AS NOE WITH ...Details: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED EXPERIMENTALLY SPECIFIED AS NOE WITH THE "SUM" AVERAGING OPTION.TEN BEST STRUCTURES SELECTED ON THE BASIS OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND FAVOURABLE NON-BONDED ENERGY WERE FURTHER OPTIMIZED WITH RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE PROPORTION 1: 4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE THEN SLOWLY COOLED TO 300K IN 2.8 PS AND EQUILIBRATED AT 300K FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO 3000 STEPS OF MINIMIZATION. THE HYDROGEN BONDS OF THE GGGG TETRADS, AND NON- CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSIY VOLUMES WERE USED AS RESTRAINTS. THE RELAXATION PATHWAYS WERE CALCULATED USING CUTOFF 4.5 ANGSTROM AND 7.25 NS ISOTROPIC CORRELATION TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.16 A. IN TWO STRUCTURES THE RESIDUES T6 AND T8 DEVIATE FROM TWO CLUSTERS FORMED BY REST OF 8 STRUCTURES, AND THESE TWO STRUCTURES WERE OMITTED FROM DEPOSITION.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE ...Conformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 8

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