5LNC

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The macro domain as fusion tag for carrier-driven crystallization.

Wild, R.Hothorn, M.

(2017) Protein Sci 26: 365-374

  • DOI: 10.1002/pro.3073
  • Primary Citation of Related Structures:  
    5LNC

  • PubMed Abstract: 
  • Obtaining well-ordered crystals remains a significant challenge in protein X-ray crystallography. Carrier-driven crystallization can facilitate crystal formation and structure solution of difficult target proteins. We obtained crystals of the small and highly flexible SPX domain from the yeast vacuolar transporter chaperone 4 (Vtc4) when fused to a C-terminal, non-cleavable macro tag derived from human histone macroH2A1 ...

    Obtaining well-ordered crystals remains a significant challenge in protein X-ray crystallography. Carrier-driven crystallization can facilitate crystal formation and structure solution of difficult target proteins. We obtained crystals of the small and highly flexible SPX domain from the yeast vacuolar transporter chaperone 4 (Vtc4) when fused to a C-terminal, non-cleavable macro tag derived from human histone macroH2A1.1. Initial crystals diffracted to 3.3 Å resolution. Reductive protein methylation of the fusion protein yielded a new crystal form diffracting to 2.1 Å. The structures were solved by molecular replacement, using isolated macro domain structures as search models. Our findings suggest that macro domain tags can be employed in recombinant protein expression in E. coli, and in carrier-driven crystallization.


    Organizational Affiliation

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar transporter chaperone 4,Core histone macro-H2A.1A, B374Saccharomyces cerevisiae S288CHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: VTC4PHM3YJL012CJ1345H2AFYMACROH2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P47075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47075 
Go to UniProtKB:  P47075
Find proteins for O75367 (Homo sapiens)
Explore O75367 
Go to UniProtKB:  O75367
PHAROS:  O75367
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.02α = 90
b = 130.05β = 90
c = 158.33γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-03 
  • Released Date: 2016-11-09 
  • Deposition Author(s): Wild, R., Hothorn, M.

Funding OrganizationLocationGrant Number
European Research CouncilSwitzerland310856

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references