5MVI | pdb_00005mvi

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb5MVI/pdb

Classification: LYASE
Organism(s): Salmonella enterica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-16 Released: 2018-02-14
Deposition Author(s): Race, P.R., Baker, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.239 (Depositor), 0.230 (DCC)
R-Value Work:
0.213 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Salmonella enterica

Race, P.R., Baker, G.E.

To be published.

Macromolecule Content

Total Structure Weight: 322.55 kDa
Atom Count: 15,106
Modeled Residue Count: 2,134
Deposited Residue Count: 2,898
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methylcitrate dehydratase	A [auth E] B [auth D] C [auth A] D [auth B] E [auth C] A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	483	Salmonella enterica	Mutation(s): 0 Gene Names: prpD, AEV26_14870 EC: 4.2.1.79 (PDB Primary Data), 4.2.1.3 (UniProt)
UniProt
Find proteins for Q8Z903 (Salmonella typhi) Explore Q8Z903 Go to UniProtKB: Q8Z903
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Z903
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.239 (Depositor), 0.230 (DCC)
R-Value Work: 0.213 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.662	α = 90
b = 139.662	β = 90
c = 513.484	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-08
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.