BMRB Entry 16226

Name: Solution Structure of cis-5R,6S-thymine glycol opposite complementary guanine in duplex DNA
Published: 2009-11-09

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PDB ID: 2kh7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16226
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of cis-5R,6S-thymine glycol opposite complementary guanine in duplex DNA

Deposition date:

2009-03-24

Original release date:

2009-11-09

Authors:

Brown, Kyle

Citation:

Citation: Brown, Kyle; Basu, Ashis; Stone, Michael. "The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA." Biochemistry 48, 9722-9733 (2009).
PubMed: 19772348

Assembly members:

Assembly members:
DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')_, polymer, 12 residues, 3392.232 Da.
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_, polymer, 12 residues, 3625.425 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')_: GTGCGXGTTTGT
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_: ACAAACGCGCAC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	230

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_(5'-D(DGPDTPDGPDCPDGP(TG)PDGPDTPDTPDTPDGPDT)-3')_	1
2	DNA_(5'-D(DAPDCPDAPDAPDAPDCPDGPDCPDGPDCPDAPDC)-3')_	2

Entities:

Entity 1, DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')_ 12 residues - 3392.232 Da.

1

DG

DT

DG

DC

DG

CTG

DG

DT

2

DG

DT

Entity 2, DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_ 12 residues - 3625.425 Da.

1

DA

DC

DA

DC

DG

DC

DG

DC

2

DA

DC

Samples:

sample_1: DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')_ 1 mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_ 1 mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 10 uM; EDTA 50 uM

sample_2: DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')_ mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_ mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 10 uM; EDTA 50 uM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1.0 atm; temperature: 303 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.0; pressure: 1.0 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 31P-1H COSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - processing

MARDIGRAS, Borgias, B.A. & James, T.L. - restraint generation

CORMA, James T.L. - structure validation

CURVES, Lavery, R. and Sklenar, H - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz