9BK4

Crystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with pyruvic acid bound

• PDB DOI: https://doi.org/10.2210/pdb9BK4/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.218 
• R-Value Work: 0.184 
• R-Value Observed: 0.188 

Starting Model: in silico

Literature

Crystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with pyruvic acid bound

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.41 kDa 
• Atom Count: 2,072 
• Modelled Residue Count: 232 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RidA family protein PA5083	A, B	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) Explore A0A069Q0R8  Go to UniProtKB:  A0A069Q0R8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PYR (Subject of Investigation/LOI)	C [auth A], E [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.218 
• R-Value Work: 0.184 
• R-Value Observed: 0.188 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.404	α = 90
b = 75.404	β = 90
c = 279.606	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release