1W0D | pdb_00001w0d

The high resolution structure of Mycobacterium tuberculosis LeuB (Rv2995c)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.241 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

The High Resolution Structure of Leub (Rv2995C) from Mycobacterium Tuberculosis

Singh, R.K., Kefala, G., Janowski, R., Mueller-Dieckmann, C., Von Kries, J.P., Weiss, M.S.

(2005) J Mol Biology 346: 1

  • DOI: https://doi.org/10.1016/j.jmb.2004.11.059
  • Primary Citation Related Structures: 
    1W0D

  • PubMed Abstract: 

    The crystal structure of the enzyme 3-isopropylmalate dehydrogenase (IPMDH) from Mycobacterium tuberculosis (LeuB, Mtb-IPMDH, Rv2995c) without substrate or co-factor was determined at 1.65 A resolution, which is the highest resolution reported for an IPMDH to date. The crystals contain two functional dimers in the asymmetric unit in an arrangement close to a tetramer of D2 symmetry. Despite the absence of a substrate or inhibitor bound to the protein, the structure of the monomer resembles the previously observed closed form of the enzyme more closely than the open form. A comparison with the substrate complex of IPMDH from Thiobacillus ferrooxidans and the co-factor complex of the Thermus thermophilus enzyme revealed a close relationship of the active-site architecture between the various bacterial enzymes. The inhibitor O-isobutenyl oxalylhydroxamate was found to bind to the active site of IPMDH in a mode similar to the substrate isopropylmalate.

    • Organizational Affiliation: 
    • EMBL Hamburg Outstation, c/o DESY, Notkestr. 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 141.84 kDa 
  • Atom Count: 10,609 
  • Modeled Residue Count: 1,348 
  • Deposited Residue Count: 1,348 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-ISOPROPYLMALATE DEHYDROGENASE
A, B, C, D
337Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 1.1.1.85
UniProt
Find proteins for P9WKK9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKK9 
Go to UniProtKB:  P9WKK9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKK9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.241 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.47α = 90
b = 97.06β = 90
c = 181.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-05-24
    Changes: Structure summary
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Other