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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Also Cited By: 4YWT

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glypican-1
A, B, C, D
478Homo sapiensMutation(s): 0 
Gene Names: GPC1
Find proteins for P35052 (Homo sapiens)
Go to Gene View: GPC1
Go to UniProtKB:  P35052
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.230α = 90.00
b = 166.720β = 90.80
c = 139.090γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Atomic model, Derived calculations, Other
  • Version 1.2: 2018-01-17
    Type: Data collection
  • Version 1.3: 2018-11-28
    Type: Data collection, Database references, Source and taxonomy, Structure summary