5YCQ

Unique Specificity-Enhancing Factor for the AAA+ Lon Protease

PDB DOI: https://doi.org/10.2210/pdb5YCQ/pdb
Entry: 5YCQ supersedes: 1VBV

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli 55989
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-08 Released: 2018-04-11
Deposition Author(s): Abe, Y., Shioi, S., Kita, S., Nakata, H., Maenaka, K., Kohda, D., Katayama, T., Ueda, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266
R-Value Work: 0.223
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation

Abe, Y., Shioi, S., Kita, S., Nakata, H., Maenaka, K., Kohda, D., Katayama, T., Ueda, T.

(2017) FEBS Lett 591: 3805-3816

PubMed: 29083032 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12892
Primary Citation of Related Structures:
5YCQ

PubMed Abstract:
The heat shock protein HspQ (YccV) of Escherichia coli has been proposed to participate in the retardation of replication initiation in cells with the dnaA508 allele. In this study, we have determined the 2.5-Å-resolution X-ray structure of the trimer of HspQ, which is also the first structure of a member of the YccV superfamily. The acidic character of the HspQ trimer suggests an interaction surface with basic proteins. From these results, we discuss the cellular function of HspQ, including its relationship with the DnaA508 protein.

Organizational Affiliation

Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.

Macromolecule Content

Total Structure Weight: 11.93 kDa
Atom Count: 609
Modelled Residue Count: 77
Deposited Residue Count: 105
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HspQ	A	105	Escherichia coli 55989	Mutation(s): 0 Gene Names: hspQ, EC55989_1015
UniProt
Find proteins for B7LE66 (Escherichia coli (strain 55989 / EAEC)) Explore B7LE66 Go to UniProtKB: B7LE66
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7LE66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266
R-Value Work: 0.223
R-Value Observed: 0.226
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.822	α = 90
b = 76.822	β = 90
c = 85.888	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

This entry supersedes: 1VBV

Revision History (Full details and data files)

Version 1.0: 2018-04-11
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

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.