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- PDB-2lzv: DNA duplex containing mispair-aligned O4U-heptylene-O4U interstra... -

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Basic information

Entry
Database: PDB / ID: 2lzv
TitleDNA duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link
ComponentsDNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')
KeywordsDNA / INTERSTRAND CROSS-LINK
Function / homologyHEPTANE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsDenisov, A.Y. / McManus, F.P. / Noronha, A.M. / Wilds, C.J.
CitationJournal: Org.Biomol.Chem. / Year: 2017
Title: Structural basis of interstrand cross-link repair by O 6 -alkylguanine DNA alkyltransferase.
Authors: Denisov, A.Y. / McManus, F.P. / O'Flaherty, D.K. / Noronha, A.M. / Wilds, C.J.
History
DepositionOct 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Source and taxonomy / Category: citation / pdbx_entity_src_syn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / struct_conn / struct_site
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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*AP*AP*UP*TP*TP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7693
Polymers6,6682
Non-polymers1001
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 20structures with the least restraint violations and the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3334.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D DQF-COSY
1412D 1H-31P HSQC
2522D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), 100% D2O100% D2O
20.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMDNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')-11
0.5 mMDNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.17.5ambient 298 K
20.17.5ambient 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity InovaVarianUnity Inova5001
Varian Unity InovaVarianUnity Inova8002
Varian VNMRSVarianVNMRS5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
VnmrJVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations and the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 11

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