1ONL

Crystal structure of Thermus thermophilus HB8 H-protein of the glycine cleavage system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method.

Nakai, T.Ishijima, J.Masui, R.Kuramitsu, S.Kamiya, N.

(2003) Acta Crystallogr.,Sect.D 59: 1610-1618


  • PubMed Abstract: 
  • The glycine-cleavage system is a multi-enzyme complex consisting of four different components (the P-, H-, T- and L-proteins). Recombinant H-protein corresponding to that from Thermus thermophilus HB8 has been overexpressed, purified and crystallized ...

    The glycine-cleavage system is a multi-enzyme complex consisting of four different components (the P-, H-, T- and L-proteins). Recombinant H-protein corresponding to that from Thermus thermophilus HB8 has been overexpressed, purified and crystallized. Synchrotron radiation from BL44B2 at SPring-8 was used to collect a native data set to 2.5 A resolution. The crystals belonged to the hexagonal space group P6(5) and contained three molecules per asymmetric unit, with a solvent content of 39%. Because of the large number of molecules within a closely packed unit cell, this structure was solved by six-dimensional molecular replacement with the program EPMR using the pea H-protein structure as a search model and was refined to an R factor of 0.189 and a free R factor of 0.256. Comparison with the pea H-protein reveals two highly conserved regions surrounding the lipoyl-lysine arm. Both of these regions are negatively charged and each has additional properties that are conserved in H-proteins from many species, suggesting that these regions are involved in intermolecular interactions. One region has previously been proposed to constitute an interaction surface with T-protein, while the other may be involved in an interaction with P-protein. Meanwhile, the lipoyl-lysine arm of the T. thermophilus H-protein was found to be more flexible than that of the pea H-protein, supporting the hypothesis that H-protein does not form a stable complex with L-protein during the reaction.


    Organizational Affiliation

    RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki, Sayo-gun, Hyogo 679-5148, Japan. nakaix@spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycine cleavage system H protein
A, B, C
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: gcvH
Find proteins for Q5SKW9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKW9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 55.775α = 90.00
b = 55.775β = 90.00
c = 191.190γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
EPMRphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance