5ECY

Structure of the Shigella flexneri VapC mutant D98N crystal form 2

PDB DOI: https://doi.org/10.2210/pdb5ECY/pdb

Classification: HYDROLASE
Organism(s): Shigella flexneri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-10-20 Released: 2016-10-19
Deposition Author(s): Xu, K., Dedic, E., Brodersen, D.E.
Funding Organization(s): Chinese Scholarship Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.180
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structural analysis on the active site architecture of an activated VapC toxin from Shigella flexneri

Xu, K., Dedic, E., Brodersen, D.E.

To be published.

Macromolecule Content

Total Structure Weight: 125.31 kDa
Atom Count: 9,609
Modelled Residue Count: 1,056
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA(fMet)-specific endonuclease VapC	A, B, C, D, E A, B, C, D, E, F, G, H	138	Shigella flexneri	Mutation(s): 1 Gene Names: vapC, mvpA, stborf2, CP0245 EC: 3.1
UniProt
Find proteins for O06662 (Shigella flexneri) Explore O06662 Go to UniProtKB: O06662
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O06662
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.180
R-Value Observed: 0.180
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.44	α = 90
b = 139.44	β = 90
c = 130.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Brodersen, D.E.

Funding Organization	Location	Grant Number
Chinese Scholarship Council	China	--

Revision History (Full details and data files)

Version 1.0: 2016-10-19
Type: Initial release
Version 1.1: 2018-01-17
Changes: Data collection
Version 2.0: 2024-05-08
Changes: Atomic model, Data collection, Database references

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.