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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.305 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Shigella flexneri Effector IpaH1880

Nishide, A., Mizushima, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.305 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Nishide, A., Mizushima, T.

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

Revision History  

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