1OBU | pdb_00001obu

Apocrustacyanin C1 crystals grown in space and earth using vapour diffusion geometry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.227 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Apocrustacyanin C(1) Crystals Grown in Space and on Earth Using Vapour-Diffusion Geometry: Protein Structure Refinements and Electron-Density Map Comparisons

Habash, J.Boggon, T.J.Raftery, J.Chayen, N.E.Zagalsky, P.F.Helliwell, J.R.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1117

  • DOI: https://doi.org/10.1107/s0907444903007959
  • Primary Citation Related Structures: 
    1OBQ, 1OBU

  • PubMed Abstract: 

    Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.


  • Organizational Affiliation
    • Department of Chemistry, University of Manchester, Manchester M13 9PL, England.

Macromolecule Content 

  • Total Structure Weight: 41.38 kDa 
  • Atom Count: 3,059 
  • Modeled Residue Count: 361 
  • Deposited Residue Count: 362 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRUSTACYANIN C1 SUBUNIT
A, B
181Homarus gammarusMutation(s): 0 
UniProt
Find proteins for P80029 (Homarus gammarus)
Explore P80029 
Go to UniProtKB:  P80029
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80029
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.018α = 90
b = 81.033β = 90
c = 110.507γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Other, Structure summary