2HR5 | pdb_00002hr5

PF1283- Rubrerythrin from Pyrococcus furiosus iron bound form

• PDB DOI: https://doi.org/10.2210/pdb2HR5/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-19 Released: 2006-10-17 
• Deposition Author(s): Dillard, B.D., Ruble, J.R., Chen, L., Liu, Z.J., Jenney Jr., F.E., Adams, M.W.W., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.176 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of iron bound Rubrerythrin from Pyrococcus Furiosus

Dillard, B.D., Clarkson, S.M., Strand, K.R., Ruble, J.R., Chen, L., Liu, Z.J., Jenney Jr., F.E., Adams, M.W.W., Rose, J.P., Wang, B.C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 39.39 kDa 
• Atom Count: 2,769 
• Modeled Residue Count: 340 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubrerythrin	A, B	171	Pyrococcus furiosus	Mutation(s): 0
UniProt
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
FE	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.176 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.402	α = 90
b = 105.402	β = 90
c = 80.095	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Dillard, B.D., Ruble, J.R., Chen, L., Liu, Z.J., Jenney Jr., F.E., Adams, M.W.W., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2012-02-22
  Changes: Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary