BMRB Entry 5245

Name: Heteroduplex of chirally pure R-methylphosphonate/DNA duplex
Published: 2002-02-08

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PDB ID: 1k1r
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR5245
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:

Heteroduplex of chirally pure R-methylphosphonate/DNA duplex

Deposition date:

2001-12-26

Original release date:

2002-02-08

Authors:

Thiviyanathan, Varatharasa; Vyazovkina, K.; Gozansky, E.; Bichenkova, E.; Abramova, T.; Luxon, B.; Lebedev, A.; Gorenstein, David

Citation:

Citation: Thiviyanathan, Varatharasa; Vyazovkina, Katya; Gozansky, E.; Bichenkova, E.; Abramova, T.; Luxon, Bruce; Lebedev, A.; Gorenstein, David. "Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry." Biochemistry 41, 827-838 (2002).
PubMed: 11790104

Assembly members:

Assembly members:
methylphosphonate, polymer, 8 residues, Formula weight is not available
methylphosphonate, polymer, 7 residues, Formula weight is not available

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):
methylphosphonate: TGTTTGGC
methylphosphonate: CXXXXXX

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1
- chemical_shift_set_2

Data type	Count
1H chemical shifts	109
31P chemical shifts	13

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	R-methylphosphonate/DNA 1	1
2	R-methylphosphonate/DNA 2	2

Entities:

Entity 1, R-methylphosphonate/DNA 1 8 residues - Formula weight is not available

1

DT

DG

DT

DG

DC

Entity 2, R-methylphosphonate/DNA 2 7 residues - Formula weight is not available

1

DC

CMR

RMP

CMR

RMP

Samples:

sample_1: methylphosphonate 1.8 mM; methylphosphonate 1.8 mM; NaCl 100 mM; phosphate 10 mM; EDTA 0.1 mM; H2O 90%; D2O 10%

sample_2: methylphosphonate 1.8 mM; methylphosphonate 1.8 mM; NaCl 100 mM; phosphate 10 mM; EDTA 0.1 mM; D2O 100%

sample_cond_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	sample_cond_1
DQF-COSY	not available	not available	sample_cond_1
2D TOCSY	not available	not available	sample_cond_1

Software:

VNMR v5.1 - data analysis

AMBER v5.0 - refinement

MORASS v2.0 - iterative matrix relaxation

NMR spectrometers:

Varian UNITYplus 400 MHz
Varian UNITYplus 750 MHz