4G3U | pdb_00004g3u

Mycobacterium smegmatis DprE1 - monoclinic crystal form

• PDB DOI: https://doi.org/10.2210/pdb4G3U/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

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

Li, H., Jogl, G.

(2013) Proteins 81: 538-543

• PubMed: 23184707 
• 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.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.88 kDa 
• Atom Count: 5,657 
• Modeled Residue Count: 692 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
oxidoreductase DprE1	A, B	403	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: MSMEG_6382 EC: 1 (PDB Primary Data), 1.1.98.3 (UniProt)
UniProt
Find proteins for A0R607 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R607  Go to UniProtKB:  A0R607

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.152	α = 90
b = 65.808	β = 109
c = 108.504	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Li, H., Jogl, G.

Revision History  

• 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, Refinement description