1R1N

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

• PDB DOI: https://doi.org/10.2210/pdb1R1N/pdb

• Classification: IRON BINDING PROTEIN
• Organism(s): Neisseria gonorrhoeae
• Mutation(s): No 


• Deposited: 2003-09-24 Released: 2004-03-09 
• Deposition Author(s): Zhu, H., Alexeev, D., Hunter, D.J., Campopiano, D.J., Sadler, P.J.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 13129433 
• DOI: https://doi.org/10.1042/BJ20031283
• Primary Citation of Related Structures:  
  1R1N


• 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) 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Biological Assembly 9  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 9 assigned by authors.

Macromolecule Content

• Total Structure Weight: 306.44 kDa 
• Atom Count: 24,350 
• Modelled Residue Count: 2,781 
• Deposited Residue Count: 2,781 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric-iron Binding Protein	A, B, C, D, E, F, G, H, I	309	Neisseria gonorrhoeae	Mutation(s): 0
UniProt
Find proteins for P17259 (Neisseria gonorrhoeae) Explore P17259  Go to UniProtKB:  P17259

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CNF	O [auth F]	OXO-IRON CLUSTER 3 Fe3 H9 O12 IYMKJKNVMFFAIB-UHFFFAOYSA-E
CN1	L [auth C], N [auth E], P [auth G], R [auth I]	OXO-IRON CLUSTER 2 Fe3 H9 O12 SUDSRVCDIHGFGD-UHFFFAOYSA-E
CNB	J [auth A], K [auth B], M [auth D], Q [auth H]	OXO-IRON CLUSTER 1 Fe3 H8 O11 HGBUJFYYDTXMPV-UHFFFAOYSA-F

Experimental Data & Validation

Experimental Data

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

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.5	α = 90
b = 146.5	β = 90
c = 114.969	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-09 
Deposition Author(s): Zhu, H., Alexeev, D., Hunter, D.J., Campopiano, D.J., Sadler, P.J.

Revision History  

• Version 1.0: 2004-03-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-12-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary