3R6M

Crystal structure of Vibrio parahaemolyticus YeaZ

PDB DOI: https://doi.org/10.2210/pdb3R6M/pdb

Classification: HYDROLASE
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-03-21 Released: 2011-09-07
Deposition Author(s): Roujeinikova, A., Aydin, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.294
R-Value Work: 0.239
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

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

Literature

Structural Analysis of the Essential Resuscitation Promoting Factor YeaZ Suggests a Mechanism of Nucleotide Regulation through Dimer Reorganization.

Aydin, I., Saijo-Hamano, Y., Namba, K., Thomas, C., Roujeinikova, A.

(2011) PLoS One 6: e23245-e23245

PubMed: 21858042 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0023245
Primary Citation of Related Structures:
3R6M

PubMed Abstract:
The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC) state.

Organizational Affiliation

Department of Microbiology, Monash University, Clayton, Victoria, Australia.

Macromolecule Content

Total Structure Weight: 91.24 kDa
Atom Count: 6,162
Modelled Residue Count: 848
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YeaZ, resuscitation promoting factor	A, B, C, D	213	Vibrio parahaemolyticus	Mutation(s): 0 Gene Names: VP0866, YeaZ
UniProt
Find proteins for Q87RD1 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87RD1 Go to UniProtKB: Q87RD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87RD1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.294
R-Value Work: 0.239
R-Value Observed: 0.241
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.733	α = 90
b = 63.844	β = 104.94
c = 82.271	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Roujeinikova, A.

Revision History (Full details and data files)

Version 1.0: 2011-09-07
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.