4G3T

Mycobacterium smegmatis DprE1 - hexagonal crystal form

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 1.1 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

  • DOI: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
oxidoreductase DprE1A403Mycolicibacterium smegmatisMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R607
Protein Feature View
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  • 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 = 64.148α = 90
b = 64.148β = 90
c = 275.462γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
XDSdata reduction
XDSdata scaling
SnBphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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

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