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 25512

Title: NMR structure of VirB9 C-terminal domain in complex with VirB7 N-terminal domain from Xanthomonas citri's T4SS.   PubMed: 27594685

Deposition date: 2015-03-03 Original release date: 2015-09-10

Authors: Oliveira, Luciana; Souza, Diorge; Salinas, Roberto; Wienk, Hans; Boelens, Rolf; Farah, Shaker

Citation: Oliveira, Luciana Coutinho; Souza, Diorge Paulo; Oka, Gabriel Umaji; Lima, Filipe da Silva; Oliveira, Ronaldo Junio; Favaro, Denize Cristina; Wienk, Hans; Boelens, Rolf; Farah, Chuck Shaker; Salinas, Roberto Kopke. "VirB7 and VirB9 Interactions Are Required for the Assembly and Antibacterial Activity of a Type IV Secretion System"  Structure 24, 1707-1718 (2016).

Assembly members:
Xac_VirB7NT, polymer, 24 residues, 2641.898 Da.
Xac_VirB9CT, polymer, 107 residues, 12471.240 Da.

Natural source:   Common Name: g-proteobacteria   Taxonomy ID: 190486   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Xanthomonas citri

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
Xac_VirB7NT: XTKPAPDFGGRWKHVNHFDE APTE
Xac_VirB9CT: GSHMNAKILKDRRYYYDYDY ATRTKKSWLIPSRVYDDGKF TYINMDLTRFPTGNFPAVFA REKEHAEDFLVNTTVEGNTL IVHGTYPFLVVRHGDNVVGL RRNKQKX

Data sets:
Data typeCount
13C chemical shifts470
15N chemical shifts114
1H chemical shifts860

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Xac_VirB7NT1
2Xac_VirB9CT2

Entities:

Entity 1, Xac_VirB7NT 24 residues - 2641.898 Da.

Modification: Acetylation (N-Terminal); Amidation (C-Terminal).

1   ACETHRLYSPROALAPROASPPHEGLYGLY
2   ARGTRPLYSHISVALASNHISPHEASPGLU
3   ALAPROTHRGLU

Entity 2, Xac_VirB9CT 107 residues - 12471.240 Da.

The first four residues (GSHM) belong to the vector encoded sequence.

1   GLYSERHISMETASNALALYSILELEULYS
2   ASPARGARGTYRTYRTYRASPTYRASPTYR
3   ALATHRARGTHRLYSLYSSERTRPLEUILE
4   PROSERARGVALTYRASPASPGLYLYSPHE
5   THRTYRILEASNMETASPLEUTHRARGPHE
6   PROTHRGLYASNPHEPROALAVALPHEALA
7   ARGGLULYSGLUHISALAGLUASPPHELEU
8   VALASNTHRTHRVALGLUGLYASNTHRLEU
9   ILEVALHISGLYTHRTYRPROPHELEUVAL
10   VALARGHISGLYASPASNVALVALGLYLEU
11   ARGARGASNLYSGLNLYSNH2

Samples:

sample_1: Xac_VirB9CT, [U-99% 13C; U-99% 15N], 0.500 mM; Xac_VirB7NT 1 mM; D2O, [U-99% 2H], 10%; sodium acetate, [U-100% 2H], 20 mM; sodium chloride 50 mM; sodium azide 1%; H2O 90%

sample_conditions_1: ionic strength: 0.07 M; pH: 5; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D CCH TOCSYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 15N, 13C CNH-NOESYsample_1isotropicsample_conditions_1
2D 13C15N filtered NOEsample_1isotropicsample_conditions_1
2D 13C,15N filtered TOCSYsample_1isotropicsample_conditions_1
3D HBCBCGCDHDsample_1isotropicsample_conditions_1
3D 15N-edited NOESYsample_1isotropicsample_conditions_1
3D 13C-edited NOESYsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HBCBCGCDCEHEsample_1isotropicsample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

TALOS, Cornilescu, Delaglio and Bax - data analysis

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

CcpNmr_Analysis v2.4.1, CCPN - data analysis

NMR spectrometers:

  • Bruker Avance III 800 MHz
  • Bruker Avance III 900 MHz

Related Database Links:

UNP Q8PJB3 Q8PJB5

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts