Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.

Kukimoto-Niino, M.Murayama, K.Inoue, M.Terada, T.Tame, J.R.Kuramitsu, S.Shirouzu, M.Yokoyama, S.

(2004) J Mol Biol 337: 761-770

  • DOI: https://doi.org/10.1016/j.jmb.2004.01.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Obg comprises a unique family of high-molecular mass GTPases conserved from bacteria to eukaryotes. Bacterial Obg is essential for cellular growth, sporulation, and differentiation. Here, we report the crystal structure of the full-length form of Obg from Thermus thermophilus HB8 at 2.07 A resolution, in the nucleotide-free state. It reveals a three-domain arrangement, composed of the N-terminal domain, the guanine nucleotide-binding domain (G domain), and the C-terminal domain. The N-terminal and G domains have the Obg fold and the Ras-like fold, respectively. These global folds are similar to those of the recently published structure of the C-terminal domain-truncated form of Obg from Bacillus subtilis. On the other hand, the C-terminal domain of Obg was found to have a novel fold (the OCT fold). A comparison of the T.thermophilus and B.subtilis nucleotide-free Obg structures revealed significant conformational changes in the switch-I and switch-II regions of the G domain. Notably, the N-terminal domain is rotated drastically, by almost 180 degrees, around the G domain axis. In the T.thermophilus Obg crystal, the nucleotide-binding site of the G domain interacts with the C-terminal domain of the adjacent molecule. These data suggest a possible domain rearrangement of Obg, and a potential role of the C-terminal domain in the regulation of the nucleotide-binding state.

  • Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
the GTP-binding protein Obg416Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q5SHE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHE9 
Go to UniProtKB:  Q5SHE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHE9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
C6 H14 O2
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.332α = 90
b = 65.332β = 90
c = 201.709γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations