5YCQ | pdb_00005ycq

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

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 
• DOI: https://doi.org/10.1002/1873-3468.12892
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.

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 Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Abe, Y., Shioi, S., Kita, S., Nakata, H., Maenaka, K., Kohda, D., Katayama, T., Ueda, T.
• This entry supersedes: 1VBV

Revision History  

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