BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 27342

Title: Backbone assignments for the N-terminal domain of VirB10   PubMed: 30349081

Authors: Oliveira, Luciana; Salinas, Roberto; Farah, Chuck

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).

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

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

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

Data sets:
Data typeCount
13C chemical shifts373
15N chemical shifts82
1H chemical shifts82
heteronuclear NOE values62

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1VirB10NT1

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   GLYSERHISMETGLNSERGLYGLUASPSER
2   ALAPROPROLYSPROARGTHRGLUTHRVAL
3   VALALAPROALALEUPROGLNSERMETTHR
4   ALAPROVALGLUGLUALAPROVALPROLEU
5   ALAGLNGLNPROSERLEUPROPROLEUPRO
6   PROMETPROTHRASPASNSERGLUGLUVAL
7   SERSERALAPROGLUARGGLNARGGLYPRO
8   THRLEULEUGLUARGARGILELEUALAGLU
9   SERALAALAASNGLYGLYGLYVALPROGLY
10   GLNLEUGLYALAGLNPROALAPROTHRGLN
11   GLUASP

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
hsqc_noe_sas_bpp_cpdssample_1isotropicsample_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

Related Database Links:

REF WP_005914234.1