BMRB Entry 27342

Name: Backbone assignments for the N-terminal domain of VirB10
Published: 2018-10-23

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27342

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:

Backbone assignments for the N-terminal domain of VirB10

Deposition date:

2017-12-19

Original release date:

2018-10-23

Authors:

Oliveira, Luciana; Salinas, Roberto; Farah, Chuck

Citation:

Citation: Sgro, German; Costa, Tiago; Cenens, Willian; Souza, Diorge; Cassago, Alexandre; Oliveira, Luciana; Salinas, Roberto; Portugal, Rodrigo; Farah, Chuck; Waksman, Gabriel. "Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri" Nat. Microbiol. 3, 1429-1440 (2018).
PubMed: 30349081

Assembly members:

Assembly members:
VirB10NT, polymer, 102 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Xanthomonas citri Taxonomy ID: 346 Superkingdom: Bacteria Kingdom: not available Genus/species: Xanthomonas citri

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28(a)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VirB10NT: GSHMQSGEDSAPPKPRTETV VAPALPQSMTAPVEEAPVPL AQQPSLPPLPPMPTDNSEEV SSAPERQRGPTLLERRILAE SAANGGGVPGQLGAQPAPTQ ED

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1

Data type	Count
13C chemical shifts	373
15N chemical shifts	82
1H chemical shifts	82
heteronuclear NOE values	62

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VirB10NT	1

Entities:

Entity 1, VirB10NT 102 residues - Formula weight is not available

The 4 first Residues (GSHM) represent a reminiscent non-native fragment from the affinity tag.

1

GLY

SER

HIS

MET

GLN

SER

GLY

GLU

ASP

SER

2

ALA

PRO

LYS

PRO

ARG

THR

GLU

THR

VAL

3

VAL

ALA

PRO

ALA

LEU

PRO

GLN

SER

MET

THR

4

ALA

PRO

VAL

GLU

ALA

PRO

VAL

PRO

LEU

5

ALA

GLN

PRO

SER

LEU

PRO

LEU

PRO

6

PRO

MET

PRO

THR

ASP

ASN

SER

GLU

VAL

7

SER

ALA

PRO

GLU

ARG

GLN

ARG

GLY

PRO

8

THR

LEU

GLU

ARG

ILE

LEU

ALA

GLU

9

SER

ALA

ASN

GLY

VAL

PRO

GLY

10

GLN

LEU

GLY

ALA

GLN

PRO

ALA

PRO

THR

GLN

11

GLU

ASP

Samples:

sample_1: VirB10NT, [U-100% 13C; U-100% 15N], 300 ± 5 uM; D2O, [U-2H], 10 ± 0.1 %; sodium acetate 20 ± 1 mM; sodium chloride 150 ± 1 mM; sodium azide 0.05 ± 0.001 %

sample_conditions_1: ionic strength: 150 mM; pH: 5.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
hsqc_noe_sas_bpp_cpds	sample_1	isotropic	sample_conditions_1

Software:

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

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

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

CCPNMR_ANALYSIS v2.4.2, Vranken et al., 2005 - chemical shift assignment, data analysis

Matlab, MathWorks - data analysis

NMR spectrometers:

Bruker Avance III 800 MHz