9G7M

Crystal structure of Collimonas fungivorans PE-like toxin, Cfx

PDB DOI: https://doi.org/10.2210/pdb9G7M/pdb

Classification: TOXIN
Organism(s): Collimonas fungivorans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-07-22 Released: 2025-01-29
Deposition Author(s): Masuyer, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 ?
R-Value Free: 0.253
R-Value Work: 0.229

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Discovery of Additional Family Members Reveals High Structural Conservation Across Mono-ADP Ribosylating Toxins

Masuyer, G., Mrsny, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 68.23 kDa
Atom Count: 4,735
Modelled Residue Count: 610
Deposited Residue Count: 625
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exotoxin A-like protein	A	625	Collimonas fungivorans	Mutation(s): 1 Gene Names: BCF11_5153
UniProt
Find proteins for A0A2A9JQY3 (Collimonas sp. PA-H2) Explore A0A2A9JQY3 Go to UniProtKB: A0A2A9JQY3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2A9JQY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 ?
R-Value Free: 0.253
R-Value Work: 0.229
Space Group: P 6₂ 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 141.797	α = 90
b = 141.797	β = 90
c = 202.661	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release

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.