Crystal structure of Thermotoga maritima ribosome biogenesis GTP-binding protein EngB (YsxC/YihA) in complex with GDP

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Structure of an essential GTPase, YsxC, from Thermotoga maritima

Chan, K.H.Wong, K.B.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 640-646

  • DOI: https://doi.org/10.1107/S1744309111011651
  • Primary Citation of Related Structures:  
    3PQC, 3PR1

  • PubMed Abstract: 

    YsxC belongs to the YihA family of TRAFAC class GTPases. The protein is involved in the biogenesis of ribosomes and is essential for the survival of a wide range of bacteria. Here, crystal structures of YsxC from Thermotoga maritima and its complex with GDP were determined at maximal resolutions of 2.3 and 1.9 Å, respectively. Major structural differences are observed in the switch I region, which is disordered in the apo form but exists in both an `open' and a `closed' conformation in the GDP-bound state. A comparison with the structure of the GMPPNP-YsxC complex from Bacillus subtilis provides insights into the mechanism of conformational change in the switch I and II regions upon hydrolysis of GTP.

  • Organizational Affiliation

    School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable GTP-binding protein engB
A, B
195Thermotoga maritimaMutation(s): 0 
Gene Names: engBTM_1466
Find proteins for Q9X1H7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1H7 
Go to UniProtKB:  Q9X1H7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1H7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.67α = 90
b = 69.714β = 90
c = 94.836γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-23
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Structure summary
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description