1FX7

CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of the iron-dependent regulator from Mycobacterium tuberculosis at 2.0-A resolution reveals the Src homology domain 3-like fold and metal binding function of the third domain.

Feese, M.D., Ingason, B.P., Goranson-Siekierke, J., Holmes, R.K., Hol, W.G.

(2001) J Biol Chem 276: 5959-5966

  • DOI: 10.1074/jbc.M007531200
  • Primary Citation of Related Structures:  
    1FX7

  • PubMed Abstract: 

    • Iron-dependent regulators are primary transcriptional regulators of virulence factors and iron scavenging systems that are important for infection by several bacterial pathogens. Here we present the 2.0-A crystal structure of the wild type iron-dependent regulator from Mycobacterium tuberculosis in its fully active holorepressor conformation ...

    Iron-dependent regulators are primary transcriptional regulators of virulence factors and iron scavenging systems that are important for infection by several bacterial pathogens. Here we present the 2.0-A crystal structure of the wild type iron-dependent regulator from Mycobacterium tuberculosis in its fully active holorepressor conformation. Clear, unbiased electron density for the Src homology domain 3-like third domain, which is often invisible in structures of iron-dependent regulators, was revealed by density modification and averaging. This domain is one of the rare examples of Src homology domain 3-like folds in bacterial proteins, and, in addition, displays a metal binding function by contributing two ligands, one Glu and one Gln, to the pentacoordinated cobalt atom at metal site 1. Both metal sites are fully occupied, and tightly bound water molecules at metal site 1 ("Water 1") and metal site 2 ("Water 2") are identified unambiguously. The main chain carbonyl of Leu4 makes an indirect interaction with the cobalt atom at metal site 2 via Water 2, and the adjacent residue, Val5, forms a rare gamma turn. Residues 1-3 are well ordered and make numerous interactions. These ordered solvent molecules and the conformation and interactions of the N-terminal pentapeptide thus might be important in metal-dependent activation.

    Organizational Affiliation: 

    Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IRON-DEPENDENT REPRESSOR IDERA, B, C, D230Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WMH1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMH1 
Go to UniProtKB:  P9WMH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMH1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
CA [auth D],
DA [auth D],
E [auth A],
F [auth A],
G [auth A],
CA [auth D],
DA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CO
Query on CO
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
EA [auth D],
FA [auth D],
GA [auth D],
AA [auth C],
BA [auth C],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
K [auth A],
L [auth A],
M [auth A],
S [auth B],
T [auth B],
U [auth B],
Z [auth C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.309α = 90
b = 113.97β = 90
c = 236.21γ = 90
Software Package:
Software NamePurpose
AMoREphasing
DMmodel building
REFMACrefinement
TNTrefinement
DENZOdata reduction
CCP4data scaling
DMphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation