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- PDB-6j37: DNA minidumbbell structure of two CTTG repeats -

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Basic information

Entry
Database: PDB / ID: 6j37
TitleDNA minidumbbell structure of two CTTG repeats
ComponentsDNA (5'-D(*CP*TP*TP*GP*CP*TP*TP*G)-3')
KeywordsDNA / minidumbbell / reverse wobble TT mispair / hydrophobic interaction
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / not applicable
AuthorsLam, S.L. / Guo, P.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2020
Title: Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell.
Authors: Guo, P. / Lam, S.L.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_last / _citation.title
Revision 1.3Apr 22, 2020Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*TP*TP*GP*CP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5708
Polymers2,4091
Non-polymers1617
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area790 Å2
ΔGint-60 kcal/mol
Surface area1590 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the least restraint violations
RepresentativeModel #1least restraint violation

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Components

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


Mass: 2408.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
121isotropic22D 1H-1H TOCSY
131isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution
Contents: 1 mM No labeling DNA, 10 mM No labeling sodium phosphate, 0.02 mM No labeling DSS, 99.96% D2O
Label: No labeling / Solvent system: 99.96% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNANo labeling1
10 mMsodium phosphateNo labeling1
0.02 mMDSSNo labeling1
Sample conditionsIonic strength: 10 mM / Ionic strength err: 0.1 / Label: condition_1 / pH: 7 / PH err: 0.1 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 273 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
TopSpinBruker Biospinchemical shift assignment
RefinementMethod: not applicable / Software ordinal: 1
NMR representativeSelection criteria: least restraint violation
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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