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- PDB-2hmd: Stereochemistry Modulates Stability of Reduced Inter-Strand Cross... -

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Basic information

Entry
Database: PDB / ID: 2hmd
TitleStereochemistry Modulates Stability of Reduced Inter-Strand Cross-Links Arising From R- and S-alpha-methyl-gamma-OH-1,N2-propano-2'-Deoxyguanine in the 5'-CpG-3' DNA Sequence
Components(DNA dodecamer with interstrand cross-link) x 2
KeywordsDNA / crotonaldehyde interstrand DNA cross-link
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry; simulated annealing; molecular dynamics; matrix relaxation
Model type detailsminimized average
AuthorsCho, Y.-J. / Kozekov, I.D. / Harris, T.M. / Rizzo, C.J. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2007
Title: Stereochemistry Modulates the Stability of Reduced Interstrand Cross-Links Arising from R- and S-alpha-CH(3)-gamma-OH-1,N(2)-Propano-2'-deoxyguanosine in the 5'-CpG-3' DNA Sequence
Authors: Cho, Y.-J. / Kozekov, I.D. / Harris, T.M. / Rizzo, C.J. / Stone, M.P.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA dodecamer with interstrand cross-link
B: DNA dodecamer with interstrand cross-link


Theoretical massNumber of molelcules
Total (without water)7,3832
Polymers7,3832
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)1 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA dodecamer with interstrand cross-link


Mass: 3691.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G7 of chain A and B linked
#2: DNA chain DNA dodecamer with interstrand cross-link


Mass: 3691.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G7 of chain A and B linked

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
2422D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM in 0.25 mL; 10 mM NaH2PO4; 0.1 M NaCl; 50 uM Na2EDTA99.996% D2O
22 mM in 0.25 mL; 10 mM NaH2PO4; 0.1 M NaCl; 50 uM Na2EDTA9:1 H2O:D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1M NaCl 7.0 1 atm303 K
20.1M NaCl 7.0 1 atm286 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.3Delaglio F et al.processing
Felix2000Accelrys, Inc.data analysis
MARDIGRAS5.2.1Borgias, B.A. et al.iterative matrix relaxation
Amber8Case et alrefinement
CORMA5.2Keepers JW et al.data analysis
RefinementMethod: distance geometry; simulated annealing; molecular dynamics; matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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