Crystal Structure of the glycerol kinase from Thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites.

Sugahara, M.Asada, Y.Morikawa, Y.Kageyama, Y.Kunishima, N.

(2008) Acta Crystallogr D Biol Crystallogr 64: 686-695

  • DOI: https://doi.org/10.1107/S0907444908009980
  • Primary Citation of Related Structures:  
    1WMM, 2DPN, 2HD9, 2ZBN

  • PubMed Abstract: 

    Protein crystallization is still a major bottleneck in structural biology. As the current methodology of protein crystallization is a type of screening, it is usually difficult to crystallize important target proteins. It was thought that hetero-epitaxic growth from the surface of a mineral crystal acting as a nucleant would be an effective enhancer of protein crystallization. However, in spite of almost two decades of effort, a generally applicable hetero-epitaxic nucleant for protein crystallization has yet to be found. Here we introduce the first candidate for a universal hetero-epitaxic nucleant, microporous zeolite: a synthetic aluminosilicate crystalline polymer with regular micropores. It promotes a form-selective crystal nucleation of proteins and acts as a crystallization catalyst. The most successful zeolite nucleant was molecular sieve type 5A with a pore size of 5 A and with bound Ca2+ ions. The zeolite-mediated crystallization improved the crystal quality in five out of six proteins tested. It provided new crystal forms with better resolution in two cases, larger crystals in one case, and zeolite-dependent crystal formations in two cases. The hetero-epitaxic growth of the zeolite-mediated crystals was confirmed by a crystal-packing analysis which revealed a layer-like structure in the crystal lattice.

  • Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinase
A, B
495Thermus thermophilusMutation(s): 0 
Find proteins for Q53W24 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53W24 
Go to UniProtKB:  Q53W24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53W24
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.991α = 90
b = 90.506β = 90
c = 182.985γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description