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 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PHFClick on this verticalbar to view detailsBest fitted HF3Click on this verticalbar to view details

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
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 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PHFClick on this verticalbar to view detailsBest fitted HF3Click on this verticalbar to view details

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