2DPN

Crystal Structure of the glycerol kinase from Thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2008) Acta Crystallogr.,Sect.D 64: 686-695

  • DOI: 10.1107/S0907444908009980
  • Primary Citation of Related Structures:  

  • 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-epit ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinase
A, B
495Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: glpK
EC: 2.7.1.30
Find proteins for Q53W24 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q53W24
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.991α = 90.00
b = 90.506β = 90.00
c = 182.985γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance