6ZTV

Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told".

Grzechowiak, M.Sekula, B.Jaskolski, M.Ruszkowski, M.

(2021) Acta Biochim Pol 68: 29-31

  • DOI: https://doi.org/10.18388/abp.2020_5501
  • Primary Citation of Related Structures:  
    6ZTV, 6ZTW, 6ZTX

  • PubMed Abstract: 

    Protein crystallographers are well aware of the trap of crystallizing E. coli proteins instead of the macromolecule of interest if heterologous recombinant protein expression in E. coli was part of the experimental pipeline. Among the well-known culprits are YodA metal-binding lipocalin (25 kDa) and YadF carbonic anhydrase (a tetramer of 25 kDa subunits). We report a novel crystal form of another such culprit, E. coli HPII catalase, which is a tetrameric protein of ~340 kDa molecular weight. HPII is likely to contaminate recombinant protein samples, co-purify, and then co-crystallize with the target proteins, especially if their masses in size exclusion chromatography are ~300-400 kDa. What makes this case more interesting but also parlous, is the fact that HPII can crystallize from very low concentrations, even well below 1 mg/mL.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase HPII
A, B, C, D
753Escherichia coli K-12Mutation(s): 1 
EC: 1.11.1.6
UniProt
Find proteins for P21179 (Escherichia coli (strain K12))
Go to UniProtKB:  P21179
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.784α = 90
b = 172.257β = 104.517
c = 123.176γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandSONATA 2018/31/D/NZ1/03630
Polish National Science CentrePolandSYMFONIA 2016/20/W/ST5/00478
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references
  • Version 1.3: 2021-03-03
    Changes: Database references
  • Version 1.4: 2021-03-31
    Changes: Database references
  • Version 1.5: 2024-01-31
    Changes: Data collection, Database references, Refinement description