4G3T

Mycobacterium smegmatis DprE1 - hexagonal crystal form

PDB DOI: https://doi.org/10.2210/pdb4G3T/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-07-15 Released: 2012-12-05
Deposition Author(s): Li, H., Jogl, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.256
R-Value Work: 0.227
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of decaprenylphosphoryl-beta- D-ribose 2'-epimerase from Mycobacterium smegmatis.

Li, H., Jogl, G.

(2013) Proteins 81: 538-543

PubMed: 23184707 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/prot.24220
Primary Citation of Related Structures:
4G3T, 4G3U

PubMed Abstract:
Decaprenylphosphoryl-β-D-ribose 2'-epimerase (DprE1) is an essential enzyme in the biosynthesis of cell wall components and a target for development of anti-tuberculosis drugs. We determined the crystal structure of a truncated form of DprE1 from Mycobacterium smegmatis in two crystal forms to up to 2.35 Å resolution. The structure extends from residue 75 to the C-terminus and shares homology with FAD-dependent oxidoreductases of the vanillyl-alcohol oxidase family including the DprE1 homologue from M. tuberculosis. The M. smegmatis DprE1 structure reported here provides further insights into the active site geometry of this tuberculosis drug target.

Organizational Affiliation

Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

Macromolecule Content

Total Structure Weight: 44.44 kDa
Atom Count: 2,695
Modelled Residue Count: 336
Deposited Residue Count: 403
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
oxidoreductase DprE1	A	403	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_6382 EC: 1
UniProt
Find proteins for A0R607 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R607 Go to UniProtKB: A0R607
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R607
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.256
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.148	α = 90
b = 64.148	β = 90
c = 275.462	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
XDS	data scaling
SnB	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2013-08-28
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.