6JHO

The complex crystal structure of Cagbeta with CagZ revealed a novel regulatory mechanism for T4SS coupling ATPase in Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb6JHO/pdb

• Classification: COUPLING PROTEIN
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2019-02-18 Released: 2020-02-19 
• Deposition Author(s): Wu, X., Zhao, Y., Sun, L., Ye, X., Jiang, M., Wang, Q., Wang, Q., Wu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

The complex crystal structure of Cagbeta with CagZ revealed a novel regulatory mechanism in VirD4 coupling ATPase

Wu, X., Zhao, Y., Sun, L., Ye, R., Wu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94.8 kDa 
• Atom Count: 6,384 
• Modelled Residue Count: 749 
• Deposited Residue Count: 836 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cag pathogenicity island protein (Cag6)	A, B	208	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP_0526
UniProt
Find proteins for O25261 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25261  Go to UniProtKB:  O25261

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cag pathogenicity island protein (Cag5)	C, D	210	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP_0524 Membrane Entity: Yes
UniProt
Find proteins for O25260 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25260  Go to UniProtKB:  O25260

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.298	α = 90
b = 96.298	β = 90
c = 212.658	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Wu, X., Zhao, Y., Sun, L., Ye, X., Jiang, M., Wang, Q., Wang, Q., Wu, Y.

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description