8K3B | pdb_00008k3b

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.243 (Depositor), 0.245 (DCC)
R-Value Work:
0.199 (Depositor), 0.208 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A071KWR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243 (Depositor), 0.245 (DCC)
R-Value Work: 0.199 (Depositor), 0.208 (DCC)
R-Value Observed: 0.201 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-12-20
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.