9BK8

Crystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with 2-ketobutyric acid bound

PDB DOI: https://doi.org/10.2210/pdb9BK8/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-04-26 Released: 2024-09-04
Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.195
R-Value Work: 0.182
R-Value Observed: 0.183

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with 2-ketobutyric acid bound

Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 12.67 kDa
Atom Count: 1,010
Modelled Residue Count: 116
Deposited Residue Count: 116
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RidA family protein PA5083	A	116	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: yabJ_3, CAZ10_01035, GNQ48_03865, GUL26_07970, IPC1295_08400, IPC737_05390, NCTC13621_05579, PA52Ts2_0667 EC: 3.5.4
UniProt
Find proteins for A0A069Q0R8 (Pseudomonas aeruginosa) Go to UniProtKB: A0A069Q0R8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2KT (Subject of Investigation/LOI) Query on 2KT 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]	2-KETOBUTYRIC ACID C₄ H₆ O₃ TYEYBOSBBBHJIV-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.195
R-Value Work: 0.182
R-Value Observed: 0.183
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.547	α = 90
b = 75.547	β = 90
c = 139.748	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-09-04
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.