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 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A novel protein-mineral interface.

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

(2003) Nat Struct Biol 10: 297-302

  • DOI: 10.1038/nsb903
  • Structures With Same Primary Citation

  • 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 PROTEINA, B, C, D, E, F, G, H, I309Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: FbpAfbpAVT05_02239WHOO_00231CWHOO_01451
Find proteins for Q50964 (Neisseria gonorrhoeae)
Explore Q50964 
Go to UniProtKB:  Q50964
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHF
Query on PHF

Download CCD File 
G, H, I
HF-OXO-PHOSPHATE CLUSTER PHF
H11 Hf5 O23 P
YWHPABBSPOVOJT-VIEZALNEDS
 Ligand Interaction
HF5
Query on HF5

Download CCD File 
A, B, C, E, F
HF OXO CLUSTER HF5
H12 Hf5 O21
GIVDBOIHCZOXMU-DYJYDONSCX
 Ligand Interaction
HF3
Query on HF3

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 
  • R-Value Observed: 0.164 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.128α = 90
b = 148.128β = 90
c = 115.842γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.4: 2019-04-03
    Changes: Data collection, Source and taxonomy