8K3B

The Pseudomonas aeruginosa RccR protein complexed with KDPG

• PDB DOI: https://doi.org/10.2210/pdb8K3B/pdb

• Classification: GENE REGULATION
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-14 Released: 2023-12-20 
• Deposition Author(s): Wang, Y.J., Wu, Z.W., Ji, Q.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

A KDPG sensor RccR governs Pseudomonas aeruginosa carbon metabolism and aminoglycoside antibiotic tolerance

Wang, Y.J., Wu, Z.W., Ji, Q.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 31.98 kDa 
• Atom Count: 2,296 
• Modelled Residue Count: 281 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MurR/RpiR family transcriptional regulator	A	293	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: ybbH
UniProt
Find proteins for A0A071KWR3 (Pseudomonas aeruginosa) Explore A0A071KWR3  Go to UniProtKB:  A0A071KWR3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ELE	B [auth A]	2-keto 3 deoxy 6 phospho gluconate C6 H11 O9 P OVPRPPOVAXRCED-WVZVXSGGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.138	α = 90
b = 81.624	β = 90
c = 137.888	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Wang, Y.J., Wu, Z.W., Ji, Q.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277078

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release