5H1A

Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2.

Akiyama, T.Yamada, Y.Takaya, N.Ito, S.Sasaki, Y.Yajima, S.

(2017) Acta Crystallogr F Struct Biol Commun 73: 16-23

  • DOI: 10.1107/S2053230X16019208

  • PubMed Abstract: 
  • The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding d ...

    The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were performed in combination with molecular replacement. CRANK2 from the CCP4 suite successfully phased and modelled the complete structure of a homotetramer composed of 1000 residues in an asymmetric unit, and the model was refined to 2.1 Å resolution. The overall structure of Mi-IclR shared the same domain combination as other known IclR structures, but the relative geometry between the DBD and SBD differs. Accordingly, the geometry of the Mi-IclR tetramer was unique: the putative substrate-binding site in each subunit is accessible from the outside of the tetramer, as opposed to buried inside as in the previously known IclR structures. These differences in the domain geometry may contribute to the transcriptional regulation of IclRs.


    Organizational Affiliation

    Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IclR transcription factor homolog
A, B, C, D
270Microbacterium sp. HM58-2Mutation(s): 0 
Find proteins for A0A161LSN6 (Microbacterium sp. HM58-2)
Go to UniProtKB:  A0A161LSN6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 90.889α = 90.00
b = 155.375β = 90.00
c = 83.262γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CRANK2phasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan15K07369

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release