1J30 | pdb_00001j30

The crystal structure of sulerythrin, a rubrerythrin-like protein from a strictly aerobic and thermoacidiphilic archaeon

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.223 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

The Crystal Structure of Sulerythrin, A Rubrerythrin-like Protein from A Strictly Aerobic Archaeon, Sulfolobus tokodaii strain 7, shows unexpected domain swapping

Fushinobu, S., Shoun, H., Wakagi, T.

(2003) Biochemistry 42: 11707-11715

  • DOI: https://doi.org/10.1021/bi034220b
  • Primary Citation Related Structures: 
    1J30

  • PubMed Abstract: 

    Sulerythrin is the first rubrerythrin-like protein to be isolated from an aerobic organism, Sulfolobus tokodaii strain 7, and it lacks a C-terminal rubredoxin-like FeS(4) domain. The protein purified from Sulfolobus cells was crystallized, and the crystal structure was determined at 1.7 A resolution. The dimer of sulerythrin exhibited "domain-swapping" at the loop connecting alphaB and alphaC, hybrid four-helix bundles consisting of alphaA/B and alphaC/D being formed. The structure and atomic identity of the binuclear metal center were determined by means of anomalous scattering analysis. The site contained 1.0 mol of hexacoordinate Fe, 0.80-0.87 mol of tetracoordinate Zn, and 0.73-0.88 mol of putative O(2) per monomer. The metal ions were found at exchanged positions compared to those in the Fe/Zn-containing rubrerythrin from Desulfovibrio vulgaris. The results demonstrate that the binuclear metal center of rubrerythrin-like proteins is plastic in its ability to bind metal ions.

    • Organizational Affiliation: 
    • Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. asfushi@mail.ecc.u-tokyo.ac.jp

Macromolecule Content 

  • Total Structure Weight: 32.5 kDa 
  • Atom Count: 2,552 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
144aa long hypothetical rubrerythrin
A, B
144Sulfurisphaera tokodaii str. 7Mutation(s): 0 
UniProt
Find proteins for F9VPE5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore F9VPE5 
Go to UniProtKB:  F9VPE5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9VPE5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.223 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.428α = 90
b = 72.428β = 90
c = 98.208γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description