Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.13 kDa 
• Atom Count: 3019 
• Residue Count: 340 
• Unique protein chains: 1

3PWF

High resolution structure of the fully reduced form of rubrerythrin from P. furiosus

• DOI: 10.2210/pdb3PWF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus furiosus
• Mutation(s): No 


• Deposited: 2010-12-08 Released: 2011-06-22 
• Deposition Author(s): Dillard, B.D., Demick, J.M., Adams, M.W., Lanzilotta, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.188 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Literature

A cryo-crystallographic time course for peroxide reduction by rubrerythrin from Pyrococcus furiosus.

Dillard, B.D., Demick, J.M., Adams, M.W., Lanzilotta, W.N.

(2011) J Biol Inorg Chem 16: 949-959

• PubMed: 21647777 
• DOI: 10.1007/s00775-011-0795-6
• Primary Citation of Related Structures:  
  3PWF, 3PZA, 3QVD, 3MPS


• PubMed Abstract: 
  

High-resolution crystal structures of Pyrococcus furiosus rubrerythrin (PfRbr) in the resting (all-ferrous) state and at time points following exposure of the crystals to hydrogen peroxide are reported. This approach was possible because of the relativity slow turnover of PfRbr at room temperature. To this end, we were able to perform time-dependent peroxide treatment of the fully reduced enzyme, under strictly anaerobic conditions, in the crystalline state. In this work we demonstrate, for the first time, that turnover of a thermophilic rubrerythrin results in approximately 2-Å movement of one iron atom in the diiron site from a histidine to a carboxylate ligand. These results confirm that, despite the domain-swapped architecture, the hyperthermophilic rubrerythrins also utilize the classic combination of iron sites together with redox-dependent iron toggling to selectively reduce hydrogen peroxide over dioxygen. In addition, we have identified previously unobserved intermediates in the reaction cycle and observed structural changes that may explain the enzyme precipitation observed for the all-iron form of PfRbr upon oxidation to the all-ferric state.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubrerythrin	A, B	170	Pyrococcus furiosus	Mutation(s): 0
Find proteins for Q9UWP7 (Pyrococcus furiosus) Explore Q9UWP7  Go to UniProtKB:  Q9UWP7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	A, B	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.188 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.87	α = 90
b = 104.87	β = 90
c = 79.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-08 
• Released Date: 2011-06-22 
Deposition Author(s): Dillard, B.D., Demick, J.M., Adams, M.W., Lanzilotta, W.N.

Revision History 

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references