BMRB Entry 15786

Name: 1H,13C and 15N NMR assignments of duck HBV primer loop of the epsilon encapsidation signal
Published: 2008-09-12

BMRB Entry DOI: doi:10.13018/BMR15786

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

1H,13C and 15N NMR assignments of duck HBV primer loop of the epsilon encapsidation signal

Deposition date:

2008-05-28

Original release date:

2008-09-12

Authors:

Van der Werf, Ramon; Girard, Frederic; Nelissen, Frank; Tessari, Marco; Wijmenga, Sybren

Citation:

Citation: Van der Werf, Ramon; Girard, Frederic; Nelissen, Frank; Tessari, Marco; Wijmenga, Sybren. "1H, 13C and 15N NMR assignments of Duck HBV primer loop of the encapsidation signal epsilon" Biomol. NMR Assignments 2, 143-145 (2008).
PubMed: 19636890

Assembly members:

Assembly members:
EDHBVwt, polymer, 37 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Hepatitis B Virus Taxonomy ID: 10407 Superkingdom: Viruses Kingdom: not available Genus/species: Orthohepadnavirus Hepatitis B Virus

Experimental source:

Experimental source: Production method: enzymatic semisynthesis Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
EDHBVwt: GGACGAUCUUUACGUCCGCU UCGGCGGACUGUCGUCC

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	187
15N chemical shifts	50
1H chemical shifts	285

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	primer_loop	1

Entities:

Entity 1, primer_loop 37 residues - Formula weight is not available

1

G

A

C

G

A

U

C

U

2

U

A

C

G

U

C

G

C

U

3

U

C

G

C

G

A

C

U

4

G

U

C

G

U

C

Samples:

unlabeled(H2O): EDHBVwt 0.19 ± 0.01 mM; sodium phosphate 10 ± 0.5 mM; EDTA 0.1 ± 0.05 mM

labeled(H2O): EDHBVwt, [U-99% 13C; U-99% 15N], 1.00 ± 0.05 mM; EDTA 0.1 ± 0.05 mM; sodium phosphate 10 ± 0.5 mM; DSS 1.5 ± 0.05 mM

unlabeled(D2O): EDHBVwt 0.19 ± 0.01 mM; sodium phosphate 10 ± 0.5 mM; EDTA 0.1 ± 0.05 mM

5C_labelled: ionic strength: 23.0 mM; pH: 6.5; pressure: 1 atm; temperature: 278 K

15C_labelled: ionic strength: 23.0 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K

25C_labelled: ionic strength: 23.0 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

5C_unlabelled: ionic strength: 12.0 mM; pH: 6.5; pressure: 1 atm; temperature: 278 K

15C_unlabelled: ionic strength: 12.0 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K

25C_unlabelled: ionic strength: 12.0 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	unlabeled(H2O)	isotropic	15C_unlabelled
2D HCCH-COSY	labeled(H2O)	isotropic	25C_labelled
2D H1/3(N1/3)C2	labeled(H2O)	isotropic	25C_labelled
2D 1H-15N HSQC	labeled(H2O)	isotropic	15C_labelled
2D 1H-1H NOESY	unlabeled(D2O)	isotropic	25C_unlabelled
2D DQF-COSY	unlabeled(D2O)	isotropic	25C_unlabelled
2D 1H-15N HSQC	labeled(H2O)	isotropic	5C_labelled
2D 1H-13C HSQC	labeled(H2O)	isotropic	15C_labelled
H5(C5)C4	labeled(H2O)	isotropic	15C_labelled
3D HCCH-TOCSY	labeled(H2O)	isotropic	25C_labelled
3D-HCN	labeled(H2O)	isotropic	25C_labelled
H1/3(N1/3)C4/6	labeled(H2O)	isotropic	25C_labelled
2D 1H-15N HSQC	labeled(H2O)	isotropic	15C_labelled

Software:

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

SPARKY, Goddard - chemical shift assignment, collection, peak picking

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Varian INOVA 800 MHz