3TNY

Structure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands

Clifton, M.C.Rupert, P.B.Hoette, T.M.Raymond, K.N.Abergel, R.J.Strong, R.K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YfiY (ABC transport system substrate-binding protein)
A
303N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SKZ
Query on SKZ

Download SDF File 
Download CCD File 
A
[2-(hydroxy-kappaO)-4-[(3-{(hydroxy-kappaO)[1-(hydroxy-kappaO)ethenyl]amino}propyl)amino]-2-{2-[(3-{(hydroxy-kappaO)[1-(hydroxy-kappaO)ethenyl]amino}propyl)amino]-2-oxoethyl}-4-oxobutanoato(6-)-kappaO]iron
Schizokinen
C16 H22 Fe N4 O9
KGGQZTFRTARRPX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.796α = 90.00
b = 47.328β = 112.88
c = 64.981γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-02 
  • Released Date: 2012-09-05 
  • Deposition Author(s): Clifton, M.C.

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references