1R1N

Tri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Oxo-iron clusters in a bacterial iron-trafficking protein: new roles for a conserved motif.

Zhu, H.Alexeev, D.Hunter, D.J.Campopiano, D.J.Sadler, P.J.

(2003) Biochem.J. 376: 35-41

  • DOI: 10.1042/BJ20031283
  • Also Cited By: 1XC1

  • PubMed Abstract: 
  • We report a set of three 1.8-1.9 A resolution X-ray crystal structures of Neisseria gonorrhoeae Fbp (ferric-ion binding protein): (i) open-cleft apo-Fbp containing bound phosphate, (ii) open-cleft mono-Fe Fbp capped by nitrilotriacetate, and (iii) op ...

    We report a set of three 1.8-1.9 A resolution X-ray crystal structures of Neisseria gonorrhoeae Fbp (ferric-ion binding protein): (i) open-cleft apo-Fbp containing bound phosphate, (ii) open-cleft mono-Fe Fbp capped by nitrilotriacetate, and (iii) open-cleft trinuclear oxo-iron Fbp, the first structure of an iron-cluster adduct of a transferrin. The nine independent molecules in the unit cells provide 'snapshots' of the versatile dynamic structural roles of the conserved dityrosyl iron-binding motif (Tyr195-Tyr196) which control the capture and, possibly, processing of iron. These findings have implications for understanding bacterial iron acquisition and dissimilation, and organic/mineral interfaces.


    Organizational Affiliation

    School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferric-iron Binding Protein
A, B, C, D, E, F, G, H, I
309Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: fbp
Find proteins for P17259 (Neisseria gonorrhoeae)
Go to UniProtKB:  P17259
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNF
Query on CNF

Download SDF File 
Download CCD File 
F
OXO-IRON CLUSTER 3
Fe3 H9 O12
IYMKJKNVMFFAIB-CNUJLZSKCD
 Ligand Interaction
CNB
Query on CNB

Download SDF File 
Download CCD File 
A, B, D, H
OXO-IRON CLUSTER 1
Fe3 H8 O11
HGBUJFYYDTXMPV-UHFFFAOYSA-F
 Ligand Interaction
CN1
Query on CN1

Download SDF File 
Download CCD File 
C, E, G, I
OXO-IRON CLUSTER 2
Fe3 H9 O12
SUDSRVCDIHGFGD-VSFFLYPWCH
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.167 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 146.500α = 90.00
b = 146.500β = 90.00
c = 114.969γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance