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- PDB-2jsk: Monomeric Human Telomere DNA Tetraplex with 3+1 Strand Fold Topol... -

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Basic information

Entry
Database: PDB / ID: 2jsk
TitleMonomeric Human Telomere DNA Tetraplex with 3+1 Strand Fold Topology, Two Edgewise Loops and Double-Chain Reversal Loop, 16 G Form 1, NMR, 10 Structures
ComponentsHUMAN TELOMERE DNA
KeywordsDNA / G-TETRAD / 3+1 STRAND FOLDING / EDGEWISE / DOUBLE-CHAIN REVERSAL LOOPS / Form 1 16BrG / 10 STRUCTURES
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION
AuthorsKuryavyi, V.V. / Phan, A.T. / Luu, K.N. / Patel, D.J.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution.
Authors: Phan, A.T. / Kuryavyi, V. / Luu, K.N. / Patel, D.J.
History
DepositionJul 7, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN TELOMERE DNA


Theoretical massNumber of molelcules
Total (without water)7,3671
Polymers7,3671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain HUMAN TELOMERE DNA


Mass: 7366.586 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
1211H-1H TOCSY
1311H-31P COSY
1411H-1H COSY
1511H-15N JRHMQC
1611H-15N HMBC

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Sample preparation

DetailsContents: 0.5-5.0 mM HUMAN TELOMERE DNA, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: HUMAN TELOMERE DNA
Sample conditionsIonic strength: 70 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA6001
BRUKER AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6Variancollection
Felix2000Accelrysdata analysis
X-PLOR3.851Brunger, A.T. et al.refinement
RefinementMethod: TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION
Software ordinal: 1
Details: AFTER DEPOSITION, THE MOLECULES WERE ENERGY MINIMIZED WITH THE ENERGY FUNCTION IMPLEMENTING GEOMETRICAL VALUES IN EFFECT AT RCSB SINCE JULY 31 2007. AS A RESULT, STRUCTURE STATISTICS FOR ...Details: AFTER DEPOSITION, THE MOLECULES WERE ENERGY MINIMIZED WITH THE ENERGY FUNCTION IMPLEMENTING GEOMETRICAL VALUES IN EFFECT AT RCSB SINCE JULY 31 2007. AS A RESULT, STRUCTURE STATISTICS FOR THIS ENTRY SLIGHTLY DEVIATES FROM THE PUBLISHED ONE, AS FOLLOWS (CURRENT VS PUBLISHED): NOE VIOLATIONS (>0.2) (0.3+-0.48) VS (0.10+-0.32); MAXIMUM VIOLATION (0.20+-0.00) VS (0.21+-0.07); RMSD OF VIOLATIONS (0.03+-0.02) VS (0.02+-0.00); BOND LENGTHS (0.005+-0.000) VS (0.004+-0.000); BOND ANGLES (0.70+-0.01) VS (0.93+-0.02); IMPROPERS (0.31+-0.01) VS (0.32+-0.02); PAIRWISE RMSD: ALL ATOMS (0.78+-0.29) VS (0.67+-0.22); ALL ATOMS EXCEPT T6,T7,A8 (0.57+-0.22) VS (0.53+-0.15).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 10

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