2GZA | pdb_00002gza

Crystal structure of the VirB11 ATPase from the Brucella Suis type IV secretion system in complex with sulphate

• PDB DOI: https://doi.org/10.2210/pdb2GZA/pdb

• Classification: HYDROLASE
• Organism(s): Brucella suis 1330
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-11 Released: 2006-07-11 
• Deposition Author(s): Hare, S., Bayliss, R., Baron, C., Waksman, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.279 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

A Large Domain Swap in the VirB11 ATPase of Brucella suis Leaves the Hexameric Assembly Intact

Hare, S., Bayliss, R., Baron, C., Waksman, G.

(2006) J Mol Biology 360: 56-66

• PubMed: 16730027 
• DOI: https://doi.org/10.1016/j.jmb.2006.04.060
• Primary Citation Related Structures: 
  2GZA


• PubMed Abstract: 
  

  VirB11 ATPases are hexameric assemblies that power type IV secretion systems in bacteria. The hexamer of Brucella suis VirB11 (BsB11), like that of the Helicobacter pylori VirB11 (Hp0525), consists of a double ring structure formed by the N-terminal and C-terminal domains of each monomer. However, the monomer differs dramatically from that of Hp0525 by a large domain swap that leaves the hexameric assembly intact but profoundly alters the nucleotide-binding site and the interface between subunits.

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Organizational Affiliation: 
• School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 122.63 kDa 
• Atom Count: 7,777 
• Modeled Residue Count: 982 
• Deposited Residue Count: 1,083 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion system protein VirB11	A, B, C	361	Brucella suis 1330	Mutation(s): 0  Gene Names: VirB11 EC: 3.6.4.6
UniProt
Find proteins for Q8FXK7 (Brucella suis biovar 1 (strain 1330)) Explore Q8FXK7  Go to UniProtKB:  Q8FXK7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.279 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.211	α = 90
b = 125.815	β = 90
c = 164.089	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
ADSC	data collection
CCP4	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Hare, S., Bayliss, R., Baron, C., Waksman, G.

Revision History  

• Version 1.0: 2006-07-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description