9F7E | pdb_00009f7e

CtdA Canavanine tRNA-editing deacetylase from Pseudomonas canavaninivorans

PDB DOI: https://doi.org/10.2210/pdb9F7E/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Pseudomonas alvandae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-05-03 Released: 2025-05-14
Deposition Author(s): Tabagari, N., Mayans, O.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: integrative
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wwPDB Validation 3D Report Full Report

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

Literature

CtdA Canavanine tRNA-editing deacetylase from Pseudomonas canavaninivorans

Tabagari, N., Mayans, O.

To be published.

Macromolecule Content

Total Structure Weight: 50.29 kDa
Atom Count: 3,971
Modeled Residue Count: 462
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CtdA Canavanyl tRNA Deacylase	A, B	231	Pseudomonas alvandae	Mutation(s): 0
UniProt
Find proteins for A0A7V8UEX6 (Pseudomonas brassicacearum subsp. neoaurantiaca) Explore A0A7V8UEX6 Go to UniProtKB: A0A7V8UEX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7V8UEX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.158 (Depositor), 0.158 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data: https://doi.org/10.5281/zenodo.11109289

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.154	α = 90
b = 77.902	β = 92.51
c = 69.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
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.