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- PDB-6xah: Structure of a Stable Interstrand DNA Crosslink Involving an dA A... -

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Basic information

Entry
Database: PDB / ID: 6xah
TitleStructure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site
Components
  • DNA (5'-D(*TP*AP*GP*AP*TP*GP*AP*AP*CP*(AAB)P*TP*AP*GP*AP*CP*AP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*GP*TP*CP*TP*AP*AP*GP*TP*TP*CP*AP*TP*CP*TP*A)-3')
KeywordsDNA / interstrand crosslink / AP site
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsKellum Jr., A.H. / Qiu, D. / Voehler, M.W. / Martin, W.J. / Gates, K.S. / Stone, M.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)RO1 ES029357 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)PO1 CA160032 United States
CitationJournal: Biochemistry / Year: 2021
Title: Structure of a Stable Interstrand DNA Cross-Link Involving a beta- N -Glycosyl Linkage Between an N 6 -dA Amino Group and an Abasic Site.
Authors: Kellum Jr., A.H. / Qiu, D.Y. / Voehler, M.W. / Martin, W. / Gates, K.S. / Stone, M.P.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,9202
Polymers10,9202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2170 Å2
ΔGint-6 kcal/mol
Surface area6910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 5480.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*AP*GP*AP*TP*GP*AP*AP*CP*(AAB)P*TP*AP*GP*AP*CP*AP*TP*A)-3')


Mass: 5439.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H NOESY
122anisotropic12D 1H-1H TOCSY
232anisotropic12D 1H-1H NOESY
141anisotropic12D 1H-1H COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM deoxyribonucleic acid, 100% D2O1H_sample_D2O100% D2O
solution2500 uM deoxyribonucleic acid, 95% H2O/5% D2O1H_sample_H2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMdeoxyribonucleic acidnatural abundance1
500 uMdeoxyribonucleic acidnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1120 mMConditions_18 1 atm298 K
2120 mMConditions_28 1 atm278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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