5KH1 | pdb_00005kh1

Shigella flexneri Effector IpaH1880

PDB DOI: https://doi.org/10.2210/pdb5KH1/pdb

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

Deposited: 2016-06-14 Released: 2017-07-12
Deposition Author(s): Nishide, A., Mizushima, T.
Funding Organization(s): Grant-in-Aid for Scientific Research (B), Grant-in-Aid for JSPS Fellows

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.305 (Depositor), 0.311 (DCC)
R-Value Work:
0.239 (Depositor), 0.243 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5KH1

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

Literature

Shigella flexneri Effector IpaH1880

Nishide, A., Mizushima, T.

To be published.

Macromolecule Content

Total Structure Weight: 66.86 kDa
Atom Count: 4,421
Modeled Residue Count: 554
Deposited Residue Count: 591
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Invasion plasmid antigen	A	591	Shigella flexneri	Mutation(s): 1 Gene Names: ipaH_4, SF1880 EC: 2.3.2.27
UniProt
Find proteins for Q83R64 (Shigella flexneri) Explore Q83R64 Go to UniProtKB: Q83R64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83R64
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.305 (Depositor), 0.311 (DCC)
R-Value Work: 0.239 (Depositor), 0.243 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.316	α = 90
b = 80.058	β = 90
c = 298.346	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
BUCCANEER	model building
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Grant-in-Aid for Scientific Research (B)	Japan	15H04341
Grant-in-Aid for JSPS Fellows	Japan	14J10879

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.