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

• PDB DOI: https://doi.org/10.2210/pdb5LNC/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-08-03 Released: 2016-11-09 
• Deposition Author(s): Wild, R., Hothorn, M.
• Funding Organization(s): European Research Council

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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 

Literature

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

Wild, R., Hothorn, M.

(2017) Protein Sci 26: 365-374

• PubMed: 27774698 
• DOI: https://doi.org/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 macroH2A1.1. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 84.47 kDa 
• Atom Count: 4,673 
• Modelled Residue Count: 731 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar transporter chaperone 4,Core histone macro-H2A.1	A, B	374	Saccharomyces cerevisiae S288C, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: VTC4, PHM3, YJL012C, J1345, H2AFY, MACROH2A1
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 GTEx:  ENSG00000113648
UniProt Groups	O75367P47075

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 = 114.02	α = 90
b = 130.05	β = 90
c = 158.33	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
European Research Council	Switzerland	310856

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description