4Z24

Mimivirus R135 (residues 51-702)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • 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 


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