3I0U | pdb_00003i0u

Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb3I0U/pdb

• Classification: LYASE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-25 Released: 2009-09-01 
• Deposition Author(s): Singer, A.U., Skarina, T., Nocek, B., Gordon, R., Lam, R., Kagan, O., Edwards, A.M., Joachimiak, A., Chirgadze, N.Y., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri

Singer, A.U., Skarina, T., Lam, R., Gordon, R., Nocek, B., Kagan, O., Edwards, A.M., Chirgadze, N.Y., Parsot, C., Arbibe, L., Savchenko, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.96 kDa 
• Atom Count: 3,207 
• Modeled Residue Count: 393 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphothreonine lyase ospF	A, B	218	Shigella flexneri	Mutation(s): 0  Gene Names: CP0010, mkaD, ospF, pWR501_0013, SFLP011 EC: 4.2.3
UniProt
Find proteins for Q8VSP9 (Shigella flexneri) Explore Q8VSP9  Go to UniProtKB:  Q8VSP9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.125	α = 90
b = 62.125	β = 90
c = 239.586	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Singer, A.U., Skarina, T., Nocek, B., Gordon, R., Lam, R., Kagan, O., Edwards, A.M., Joachimiak, A., Chirgadze, N.Y., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations