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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 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 desiccatio ...

    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, Yamadaoka 1-6, Suita, Osaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b5 heme-binding domain-containing proteinA112Ramazzottius varieornatusMutation(s): 0 
Gene Names: RvY_13572-1RvY_13572.1RvY_13572
Find proteins for A0A1D1VNB4 (Ramazzottius varieornatus)
Explore A0A1D1VNB4 
Go to UniProtKB:  A0A1D1VNB4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 

  • 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