8CB2 | pdb_00008cb2

A complex of cagX and cagY components of Helicobacter pylori type IV secretion system

PDB DOI: https://doi.org/10.2210/pdb8CB2/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Helicobacter pylori
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-25 Released: 2024-02-07
Deposition Author(s): Isupov, M.N., Jiang, M., Zhang, H., Wu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.298 (Depositor), 0.298 (DCC)
R-Value Work:
0.252 (Depositor), 0.252 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 8CB2

This is version 1.0 of the entry. See complete history.

Literature

A complex of cagX and cagY components of Helicobacter pylori type IV secretion system

Isupov, M.N., Jiang, M.

To be published.

Macromolecule Content

Total Structure Weight: 95.39 kDa
Atom Count: 6,032
Modeled Residue Count: 773
Deposited Residue Count: 856
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cag pathogenicity island protein	A [auth AAA], C [auth CCC]	164	Helicobacter pylori	Mutation(s): 0 Gene Names: HP0528
UniProt
Find proteins for Q75X32 (Helicobacter pylori) Explore Q75X32 Go to UniProtKB: Q75X32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q75X32
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion system apparatus protein CagY (Fragment)	B [auth BBB], D [auth DDD]	264	Helicobacter pylori	Mutation(s): 0 Gene Names: cagY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth CCC] MOL2 format, chain E [auth CCC] mmCIF format, chain E [auth CCC]	E [auth CCC]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth CCC] Interactions & Density Focus chain E [auth CCC]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.298 (Depositor), 0.298 (DCC)
R-Value Work: 0.252 (Depositor), 0.252 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.059	α = 90
b = 196.123	β = 90
c = 200.128	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing
MOLREP	phasing
DM	phasing
Coot	model building
BUSTER	refinement
ISOLDE	refinement

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release

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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.