BMRB Entry 51612

Name: Uracil-DNA glycosylase efficiency is modulated by substrate rigidity
Published: 2023-03-14

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51612

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Uracil-DNA glycosylase efficiency is modulated by substrate rigidity

Deposition date:

2022-09-02

Original release date:

2023-03-14

Authors:

Orndorff, Paul; Poddar, Souvik; Owens, Aerial; Kumari, Nikita; Ugaz, Bryan; Amin, Samrat; Van Horn, Wade; van der Vaart, Arjan; Levitus, Marcia

Citation:

Citation: Orndorff, Paul; Poddar, Souvik; Owens, Aerial; Kumari, Nikita; Ugaz, Bryan; Amin, Samrat; Van Horn, Wade; van der Vaart, Arjan; Levitus, Marcia. "Uracil-DNA glycosylase efficiency is modulated by substrate rigidity" Sci. Rep. 13, 3915-3915 (2023).
PubMed: 36890276

Assembly members:

Assembly members:
entity_1, polymer, 13 residues, Formula weight is not available
entity_2, polymer, 13 residues, Formula weight is not available
entity_3, polymer, 13 residues, Formula weight is not available
entity_4, polymer, 13 residues, Formula weight is not available
entity_5, polymer, 13 residues, Formula weight is not available
entity_6, polymer, 13 residues, Formula weight is not available
entity_7, polymer, 13 residues, Formula weight is not available
entity_8, polymer, 13 residues, Formula weight is not available
entity_9, polymer, 13 residues, Formula weight is not available
entity_10, polymer, 13 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: obtained from a vendor

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTGAAAUTGTTAC
entity_2: GTAACAATTTCAC
entity_3: GTGAATUAGTTAC
entity_4: GTAACTAATTCAC
entity_5: GTGAAAUAGTTAC
entity_6: GTAACTATTTCAC
entity_7: GTGAATUTGTTAC
entity_8: GTAACAAATTCAC
entity_9: GTGCAAUTATGAC
entity_10: GTCATAATTGCAC

Data sets:

H_exch_rates

Data type	Count
H exchange rates	38

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	4ATF	1
2	4ATR	2
3	4TAF	3
4	4TAR	4
5	4AAF	5
6	4AAR	6
7	4TTF	7
8	4TTR	8
9	1ATF	9
10	1ATR	10

Entities:

Entity 1, 4ATF 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DG

DA

DU

DT

DG

DT

2

DT

DA

DC

Entity 2, 4ATR 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DA

DC

DA

DT

2

DC

DA

DC

Entity 3, 4TAF 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DG

DA

DT

DU

DA

DG

DT

2

DT

DA

DC

Entity 4, 4TAR 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DA

DC

DT

DA

DT

2

DC

DA

DC

Entity 5, 4AAF 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DG

DA

DU

DA

DG

DT

2

DT

DA

DC

Entity 6, 4AAR 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DA

DC

DT

DA

DT

2

DC

DA

DC

Entity 7, 4TTF 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DG

DA

DT

DU

DT

DG

DT

2

DT

DA

DC

Entity 8, 4TTR 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DA

DC

DA

DT

2

DC

DA

DC

Entity 9, 1ATF 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DG

DC

DA

DU

DT

DA

DT

2

DG

DA

DC

Entity 10, 1ATR 13 residues - Formula weight is not available

complement strand pairs A with U

1

DG

DT

DC

DA

DT

DA

DT

DG

2

DC

DA

DC

Samples:

sample_1: 4ATF 3 mM; 4ATR 3 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 50 uM

sample_2: 4TAF 3 mM; 4TAR 3 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 50 uM

sample_3: 4AAF 3 mM; 4AAR 3 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 50 uM

sample_4: 4TTF 3 mM; 4TTR 3 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 50 uM

sample_5: 1ATF 3 mM; 1ATR 3 mM; sodium phosphate 20 mM; sodium chloride 100 mM; EDTA 50 uM

sample_conditions_1: pH: 7.0; temperature: 293.15 K

sample_conditions_2: pH: 7.0; temperature: 293.15 K

sample_conditions_3: pH: 7.0; temperature: 293.15 K

sample_conditions_4: pH: 7.0; temperature: 293.15 K

sample_conditions_5: pH: 7.0; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_4
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_5
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_2	isotropic	sample_conditions_2
T1/R1 relaxation	sample_3	isotropic	sample_conditions_3
T1/R1 relaxation	sample_4	isotropic	sample_conditions_4
T1/R1 relaxation	sample_5	isotropic	sample_conditions_5

Software:

TOPSPIN v4.1 - chemical shift assignment, collection, processing

MATLAB v2019b - data analysis, processing

NMR spectrometers:

Bruker AVANCE III 850 MHz
Bruker AVANCE III 600 MHz