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


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1038/nsb903
  • Primary Citation of Related Structures:  
    1O7T

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IRON BINDING PROTEIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I
309Neisseria gonorrhoeaeMutation(s): 0 
UniProt
Find proteins for Q50964 (Neisseria gonorrhoeae)
Explore Q50964 
Go to UniProtKB:  Q50964
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50964
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHF
Query on PHF

Download Ideal Coordinates CCD File 
P [auth G],
Q [auth H],
R [auth I]
HF-OXO-PHOSPHATE CLUSTER PHF
H11 Hf5 O23 P
YWHPABBSPOVOJT-UHFFFAOYSA-A
HF5
Query on HF5

Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
L [auth C],
N [auth E],
O [auth F]
HF OXO CLUSTER HF5
H12 Hf5 O21
GIVDBOIHCZOXMU-UHFFFAOYSA-B
HF3
Query on HF3

Download Ideal Coordinates CCD File 
M [auth D]SMALLEST HF-OXO-PHOSPHATE CLUSTER HF3
H7 Hf3 O15 P
RDEYJDUCCAQDEG-UHFFFAOYSA-D
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description