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- PDB-5uzi: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damag... -

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Entry
Database: PDB / ID: 5uzi
TitleInsights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure
Components
  • DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3')
KeywordsDNA / Hoogsteen base pairs / DNA structure and dynamics / N1-methyladenine / Damage recognition and repair / NMR structure and dynamic ensembles
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsSathyamoorthy, B. / Shi, H. / Xue, Y. / Al-Hashimi, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103297 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.
Authors: Sathyamoorthy, B. / Shi, H. / Zhou, H. / Xue, Y. / Rangadurai, A. / Merriman, D.K. / Al-Hashimi, H.M.
History
DepositionFeb 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3')
B: DNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3392
Polymers7,3392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 256structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 3659.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3')


Mass: 3679.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N SOFAST-HMQC
121isotropic12D 1H-13C SOFAST-HMQC
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-1H NOESY
151isotropic22D 1H-1H TOCSY
161isotropic22D DQF-COSY
171isotropic22D 1H-31P HSQC
181isotropic12D 1H-13C TROSY
292anisotropic12D 1H-13C TROSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution13.0 mM DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'), 90% H2O/10% D2O15 mM sodium phosphate buffer pH 6.8, 25 mM NaCl, 0.1 mM EDTA, 10% D2OA6-DNAm1A1690% H2O/10% D2O
solution23.0 mM DNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3'), 90% H2O/10% D2O15 mM sodium phosphate buffer pH 6.8, 25 mM NaCl, 0.1 mM EDTA, 10% D2O, 25 mg/mL Pf1 phageA6-DNAm1A16_Pf190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.0 mMDNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3')natural abundance1
3.0 mMDNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3')natural abundance1
3.0 mMDNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3')natural abundance2
3.0 mMDNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3')natural abundance2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
115 mM sodium phosphate buffer pH 6.8, 25 mM NaCl, 0.1 mM EDTA, 10% D2O100 mMisotropic6.81 atm298 K
215 mM sodium phosphate buffer pH 6.8, 25 mM NaCl, 0.1 mM EDTA, 10% D2O, 25 mg/mL Pf1 phage100 mManisotropic6.81 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AVANCE IIBrukerAVANCE II6002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyNMRFAMGoddardchemical shift assignment
VNMRVariancollection
TopSpinBruker Biospincollection
SparkyNMRFAMGoddarddata analysis
SparkyNMRFAMGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 10

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