Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72743.45 
• Atom Count: 4839 
• Residue Count: 660 
• Unique protein chains: 1

3WAE

X-ray structure of Fe(III)-bicarbonates-ttfbpa, a ferric ion-binding protein from thermus thermophilus HB8

• DOI: 10.2210/pdb3WAE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
• Expression System: Escherichia coli


• Deposited: 2013-05-02 Released: 2014-05-21 
• Deposition Author(s): Wang, S., Ogata, M., Horita, S., Ohtsuka, J., Nagata, K., Tanokura, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 

Literature

A novel mode of ferric ion coordination by the periplasmic ferric ion-binding subunit FbpA of an ABC-type iron transporter from Thermus thermophilus HB8.

Wang, S., Ogata, M., Horita, S., Ohtsuka, J., Nagata, K., Tanokura, M.

(2014) Acta Crystallogr.,Sect.D 70: 196-202

• PubMed: 24419392 
• DOI: 10.1107/S1399004713026333
• Primary Citation of Related Structures:  
  3WAF


• PubMed Abstract: 
  

Crystal structures of FbpA, the periplasmic ferric ion-binding protein of an iron-uptake ABC transporter, from Thermus thermophilus HB8 (TtFbpA) have been solved in apo and ferric ion-bound forms at 1.8 and 1.7 Å resolution, respectively. The latter crystal structure shows that the bound ferric ion forms a novel six-coordinated complex with three tyrosine side chains, two bicarbonates and a water molecule in the metal-binding site. The results of gel-filtration chromatography and dynamic light scattering show that TtFbpA exists as a monomer in solution regardless of ferric ion binding and that TtFbpA adopts a more compact conformation in the ferric ion-bound state than in the apo state in solution.

---

Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
IRON ABC TRANSPORTER, PERIPLASMIC IRON-BINDING PROTEIN	A, B	330	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0
Find proteins for Q5SHV2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHV2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BCT	A, B	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE	A, B	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 40.170	α = 90.00
b = 101.020	β = 90.00
c = 134.610	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
XDSME	data scaling
XDSME	data reduction
PHASER	phasing
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-02 
• Released Date: 2014-05-21 
• Deposition Author(s): Wang, S., Ogata, M., Horita, S., Ohtsuka, J., Nagata, K., Tanokura, M.

Revision History 

• Version 1.0: 2014-05-21
  Type: Initial release