4YNX

Structure of YdiE from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.171 

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This is version 1.1 of the entry. See complete history

Literature

The crystal and solution structure of YdiE from Escherichia coli

Nishimura, K.Addy, C.Shrestha, R.Voet, A.R.Zhang, K.Y.J.Ito, Y.Tame, J.R.H.

(2015) Acta Crystallogr.,Sect.F 71: 919-924

  • DOI: 10.1107/S2053230X15009140

  • PubMed Abstract: 
  • Iron-containing porphyrins are essential for all life as electron carriers. Since iron is poorly available in an oxidizing environment, bacterial growth may be restricted by iron limitation, and this has led to the evolution of a huge variety of iron ...

    Iron-containing porphyrins are essential for all life as electron carriers. Since iron is poorly available in an oxidizing environment, bacterial growth may be restricted by iron limitation, and this has led to the evolution of a huge variety of iron-uptake systems. Among pathogens, iron scavenging from the haemoglobin of an animal host is a common means of acquiring sufficient iron for growth. The Isd system of Staphylococcus aureus is a well studied example; the bacterium devotes considerable resources to the construction of surface proteins that deftly remove haem from haemoglobin and pass it along a chain of related proteins, eventually delivering the haem to the cytoplasm, where it can be utilized or degraded. All organisms, however, must deal with haem and related molecules, which are by their nature hydrophobic and prone to precipitate, and which tend to promote the formation of reactive oxygen species. Chaperones are an obvious solution to the problem of maintaining a pool of haem for insertion into cytochromes without allowing naked haem to cause damage. YdiE is a very small protein from Escherichia coli of only 63 residues which may play a role in haem trafficking. Here, NMR analysis and the crystal structure of the protein to high resolution are reported.


    Organizational Affiliation

    Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.,Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YdiE
A, B
66Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ydiE
Find proteins for P0ACX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACX9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.736α = 90.00
b = 38.189β = 90.00
c = 54.728γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references