BMRB Entry 17257

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17257
MolProbity Validation Chart

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Title:
NMR structure of the Xanthomonas VirB7
Deposition date:
2010-10-15
Original release date:
2011-05-19
Authors:
Souza, Diorge; Farah, Chuck; Salinas, Roberto
Citation:

Citation: Souza, Diorge; Andrade, Maxuel; Alvarez-Martinez, Cristina; Arantes, Guilherme; Farah, Chuck; Salinas, Roberto. "A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins."  PLoS Pathog. 7, .-. (2011).
PubMed: 21589901

Assembly members:

Assembly members:
VirB7-Xac2622, polymer, 120 residues, 12871.521 Da.

Natural source:

Natural source:   Common Name: Xanthomonas axonopodis pv. citri   Taxonomy ID: 92829   Superkingdom: bacteria   Kingdom: not available   Genus/species: Xanthomonas axonopodis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VirB7-Xac2622: GSHMTKPAPDFGGRWKHVNH FDEAPTEIPLYTSYTYQATP MDGTLKTMLERWAADSNMQL SYNLPSDYTLIGPVSAISTT SVQQAATELSAVYAAQGVSV SVSANKLLVQPVPVSSGAKL

Data sets:
Data typeCount
13C chemical shifts518
15N chemical shifts122
1H chemical shifts804

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1VirB7-Xac2622 monomer1

Entities:

Entity 1, VirB7-Xac2622 monomer 120 residues - 12871.521 Da.

The first four residues (20-23) are derived from the non-native affinity tag. Residues 24-139 correspond to the predicted soluble region of VirB7-Xac2622. The native protein would be anchored via a lipidated cys residue at position 22. The native residues 1-23 are not present in this construct.

1   GLYSERHISMETTHRLYSPROALAPROASP
2   PHEGLYGLYARGTRPLYSHISVALASNHIS
3   PHEASPGLUALAPROTHRGLUILEPROLEU
4   TYRTHRSERTYRTHRTYRGLNALATHRPRO
5   METASPGLYTHRLEULYSTHRMETLEUGLU
6   ARGTRPALAALAASPSERASNMETGLNLEU
7   SERTYRASNLEUPROSERASPTYRTHRLEU
8   ILEGLYPROVALSERALAILESERTHRTHR
9   SERVALGLNGLNALAALATHRGLULEUSER
10   ALAVALTYRALAALAGLNGLYVALSERVAL
11   SERVALSERALAASNLYSLEULEUVALGLN
12   PROVALPROVALSERSERGLYALALYSLEU

Samples:

sample_1: VirB7 - Xac2622, [U-99% 13C; U-99% 15N], 0.2 mM; sodium acetate, [U-99% 2H], 10 mM; sodium chloride 50 mM; H2O 93%; D2O 7%

sample_2: VirB7 - Xac2622, [U-99% 13C; U-99% 15N], 0.2 mM; sodium acetate, [U-99% 2H], 10 mM; sodium chloride 50 mM; D2O 100%

sample_conditions_1: ionic strength: 0.06 M; pH: 5.0; pressure: 1 atm; temperature: 313 K

sample_conditions_2: ionic strength: 0.06 M; pH: 5.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQC J-modulatedsample_1anisotropicsample_conditions_2

Software:

NMRPipe v97.027.12.56, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

ANALYSIS vVersion 1.0. Release 15, CCPN - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - dihedral angle prediction

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

HADDOCK v2.0, Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin - refinement

PALES v2.1, Markus Zweckstetter, Ad Bax - RDC data analysis

MODULE2 v2, Patrice Dosset, Martin Blackledge - RDC data analysis

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

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Varian INOVA 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
EMBL CAJ24488 CCF70408 CCG39329 CDF62143 CDN21695
GB AAM37471 AGH78108 AGI08427 AJD69220 AJY82742
REF WP_005914237 WP_033836637 WP_039430902 WP_042598437

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks