1XC1

Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (FBP)

• PDB DOI: https://doi.org/10.2210/pdb1XC1/pdb

• Classification: METAL TRANSPORT
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-31 Released: 2004-09-21 
• Deposition Author(s): Zhong, W., Alexeev, D., Harvey, I., Guo, M., Hunter, D.J.B., Zhu, H., Campopiano, D.J., Sadler, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.275 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Assembly of an Oxo-Zirconium(IV) Cluster in a Protein Cleft

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

(2004) Angew Chem Int Ed Engl 43: 5914-5918

• PubMed: 15472987 
• DOI: https://doi.org/10.1002/anie.200460806
• Primary Citation of Related Structures:  
  1XC1

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Organizational Affiliation: 

School of Chemistry, King's Buildings, The University of Edinburgh, West Mains Road, Edinburgh EH93JJ, 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: 308.38 kDa 
• Atom Count: 22,547 
• 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
periplasmic iron-binding protein	A, B, C, D, E, F, G, H, I	309	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names: FBPA
UniProt
Find proteins for P17259 (Neisseria gonorrhoeae) Explore P17259  Go to UniProtKB:  P17259

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZRC	J [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth G], Q [auth H], R [auth I]	OXO ZIRCONIUM(IV) CLUSTER O17 P Zr3 WBTZCCQRTTWINH-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.275 (Depositor) 
• R-Value Work:  0.191 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.2	α = 90
b = 146.2	β = 90
c = 113.558	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Zhong, W., Alexeev, D., Harvey, I., Guo, M., Hunter, D.J.B., Zhu, H., Campopiano, D.J., Sadler, P.J.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description