1O7T

Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Protein-Mineral Interface

Alexeev, D.Zhu, H.Guo, M.Zhong, W.Hunter, D.J.B.Yang, W.Campopiano, D.J.Sadler, P.J.

(2003) Nat.Struct.Mol.Biol. 10: 297

  • DOI: 10.1038/nsb903

  • PubMed Abstract: 
  • Transferrins transport Fe3+ and other metal ions in mononuclear-binding sites. We present the first evidence that a member of the transferrin superfamily is able to recognize multi-nuclear oxo-metal clusters, small mineral fragments that are the most ...

    Transferrins transport Fe3+ and other metal ions in mononuclear-binding sites. We present the first evidence that a member of the transferrin superfamily is able to recognize multi-nuclear oxo-metal clusters, small mineral fragments that are the most abundant forms of many metals in the environment. We show that the ferric ion-binding protein from Neisseria gonorrhoeae (nFbp) readily binds clusters of Fe3+, Ti4+, Zr4+ or Hf4+ in solution. The 1.7 A resolution crystal structure of Hf-nFbp reveals three distinct types of clusters in an open, positively charged cleft between two hinged protein domains. A di-tyrosyl cluster nucleation motif (Tyr195-Tyr196) is situated at the bottom of this cleft and binds either a trinuclear oxo-Hf cluster, which is capped by phosphate, or a pentanuclear cluster, which in turn can be capped with phosphate. This first high-resolution structure of a protein-mineral interface suggests a novel metal-uptake mechanism and provides a model for protein-mediated mineralization/dissimilation, which plays a critical role in geochemical processes.


    Organizational Affiliation

    Institute of Cell and Molecular Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IRON BINDING PROTEIN
A, B, C, D, E, F, G, H, I
309Neisseria gonorrhoeaeGene Names: FbpA
Find proteins for Q50964 (Neisseria gonorrhoeae)
Go to UniProtKB:  Q50964
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HF5
Query on HF5

Download SDF File 
Download CCD File 
A, B, C, E, F
HF OXO CLUSTER HF5
H12 Hf5 O21
GIVDBOIHCZOXMU-DYJYDONSCX
 Ligand Interaction
PHF
Query on PHF

Download SDF File 
Download CCD File 
G, H, I
HF-OXO-PHOSPHATE CLUSTER PHF
H11 Hf5 O23 P
YWHPABBSPOVOJT-VIEZALNEDS
 Ligand Interaction
HF3
Query on HF3

Download SDF File 
Download CCD File 
D
SMALLEST HF-OXO-PHOSPHATE CLUSTER HF3
H7 Hf3 O15 P
RDEYJDUCCAQDEG-WCQCRJDPCG
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.164 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 148.128α = 90.00
b = 148.128β = 90.00
c = 115.842γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance