7BWH

Soluble cytochrome b5 from Ramazzottius varieornatus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of cytochrome b5unique to tardigrades.

Fukuda, Y., Kim, J., Inoue, T.

(2020) Protein Sci 29: 1829-1835

  • DOI: https://doi.org/10.1002/pro.3896
  • Primary Citation of Related Structures:  
    7BWH

  • PubMed Abstract: 

    Cytochrome b 5 is an essential electron transfer protein, which is ubiquitously found in living systems and involved in wide variety of biological processes. Tardigrades (also known as water bears), some of which are famous for desiccation resistance, have many proteins unique to them. Here, we report spectroscopic and structural characterization of a cytochrome b 5 like protein from one of the desiccation-tolerant tardigrades, Ramazzottius varieornatus strain YOKOZUNA-1 (RvCytb 5 ). A 1.4 Å resolution crystal structure revealed that RvCytb 5 is a new cytochrome b 5 protein specific to tardigrades.

    • Organizational Affiliation: 

    Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b5 heme-binding domain-containing protein112Ramazzottius varieornatusMutation(s): 0 
Gene Names: RvY_13572-1, RvY_13572.1, RvY_13572
UniProt
Find proteins for A0A1D1VNB4 (Ramazzottius varieornatus)
Explore A0A1D1VNB4 
Go to UniProtKB:  A0A1D1VNB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D1VNB4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.004α = 90
b = 37.495β = 90
c = 77.546γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJAX191C

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-08-05
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references