9BK4 | pdb_00009bk4

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A069Q0R8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PYR (Subject of Investigation/LOI) Query on PYR Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.218 (Depositor), 0.219 (DCC)
R-Value Work: 0.184 (Depositor), 0.184 (DCC)
R-Value Observed: 0.188 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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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.