4Z24

Mimivirus R135 (residues 51-702)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.204 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

A Mimivirus Enzyme that Participates in Viral Entry.

Klose, T.Herbst, D.A.Zhu, H.Max, J.P.Kenttamaa, H.I.Rossmann, M.G.

(2015) Structure 23: 1058-1065

  • DOI: https://doi.org/10.1016/j.str.2015.03.023
  • Primary Citation of Related Structures:  
    4Z24, 4Z25, 4Z26

  • PubMed Abstract: 

    Mimivirus was initially identified as a bacterium because its dense, 125-nm-long fibers stained Gram-positively. These fibers probably play a role during the infection of some host cells. The normal hosts of Mimivirus are unknown, but in the laboratory Mimivirus is usually propagated in amoeba. The structure of R135, a major component of the fibrous outer layer of Mimivirus, has been determined to 2-Å resolution. The protein's structure is similar to that of members of the glucose-methanol-choline oxidoreductase family, which have an N-terminal FAD binding domain and a C-terminal substrate recognition domain. The closest homolog to R135 is an aryl-alcohol oxidase that participates in lignin biodegradation of plant cell walls. Thus R135 might participate in the degradation of their normal hosts, including some lignin-containing algae.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-2032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GMC-type oxidoreductase R135
A, B
652Acanthamoeba polyphaga mimivirusMutation(s): 0 
Gene Names: MIMI_R135
EC: 1
UniProt
Find proteins for Q5UPL2 (Acanthamoeba polyphaga mimivirus)
Explore Q5UPL2 
Go to UniProtKB:  Q5UPL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UPL2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.76α = 111.22
b = 77.5β = 109.64
c = 94.34γ = 94.56
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI011219

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-06-03
    Changes: Database references, Structure summary
  • Version 1.2: 2015-06-10
    Changes: Database references
  • Version 1.3: 2015-06-17
    Changes: Database references
  • Version 1.4: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description