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)

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)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8VSP9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

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Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Chirgadze, N.Y.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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

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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.