3CYV

Crystal structure of uroporphyrinogen decarboxylase from Shigella flexineri: new insights into its catalytic mechanism

PDB DOI: https://doi.org/10.2210/pdb3CYV/pdb

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

Deposited: 2008-04-26 Released: 2009-04-28
Deposition Author(s): Liu, H., Zhou, H., Bi, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282
R-Value Work: 0.227
R-Value Observed: 0.227

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of uroporphyrinogen III decarboxylase from Shigella flexineri: new insights into its catalytic mechanism

Liu, H., Zhou, H., Bi, R.

To be published.

Macromolecule Content

Total Structure Weight: 39.27 kDa
Atom Count: 2,972
Modelled Residue Count: 352
Deposited Residue Count: 354
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A	354	Shigella flexneri	Mutation(s): 0 Gene Names: urod EC: 4.1.1.37
UniProt
Find proteins for Q83PB7 (Shigella flexneri) Explore Q83PB7 Go to UniProtKB: Q83PB7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q83PB7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282
R-Value Work: 0.227
R-Value Observed: 0.227
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.406	α = 90
b = 136.17	β = 90
c = 77.845	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description

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.