6JHO | pdb_00006jho

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.191 (Depositor), 0.194 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25261
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25260
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.191 (Depositor), 0.194 (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

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Entry History

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.