4BWE

Crystal structure of C-terminally truncated glypican-1 after controlled dehydration to 86 percent relative humidity

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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This is version 1.4 of the entry. See complete history. 


Literature

Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration.

Awad, W., Svensson Birkedal, G., Thunnissen, M.M., Mani, K., Logan, D.T.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2524-2533

  • DOI: 10.1107/S0907444913025250
  • Primary Citation of Related Structures:  
    4BWE

  • PubMed Abstract: 

    • The use of controlled dehydration for improvement of protein crystal diffraction quality is increasing in popularity, although there are still relatively few documented examples of success. A study has been carried out to establish whether controlled dehydration could be used to improve the anisotropy of crystals of the core protein of the human proteoglycan glypican-1 ...

    The use of controlled dehydration for improvement of protein crystal diffraction quality is increasing in popularity, although there are still relatively few documented examples of success. A study has been carried out to establish whether controlled dehydration could be used to improve the anisotropy of crystals of the core protein of the human proteoglycan glypican-1. Crystals were subjected to controlled dehydration using the HC1 device. The optimal protocol for dehydration was developed by careful investigation of the following parameters: dehydration rate, final relative humidity and total incubation time Tinc. Of these, the most important was shown to be Tinc. After dehydration using the optimal protocol the crystals showed significantly reduced anisotropy and improved electron density, allowing the building of previously disordered parts of the structure.

    Related Citations: 
    • Crystal Structure of N-Glycosylated Human Glypican-1 Core Protein: Structure of Two Loops Evolutionarily Conserved in Vertebrate Glypican-1
      Svensson, G., Awad, W., Hakansson, M., Mani, K., Logan, D.T.
      (2012) J Biol Chem 287: 14040
    Organizational Affiliation: 

    Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, 221 00 Lund, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glypican-1A, B, C, D478Homo sapiensMutation(s): 0 
Gene Names: GPC1
UniProt & NIH Common Fund Data Resources
Find proteins for P35052 (Homo sapiens)
Explore P35052 
Go to UniProtKB:  P35052
PHAROS:  P35052
GTEx:  ENSG00000063660
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.23α = 90
b = 166.72β = 90.8
c = 139.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Atomic model, Derived calculations, Other
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2018-11-28
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary