3PQC

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

• PDB DOI: https://doi.org/10.2210/pdb3PQC/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-26 Released: 2011-06-08 
• Deposition Author(s): Chan, K.H., Wong, K.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.232 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

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

• PubMed: 21636901 
• 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.07 kDa 
• Atom Count: 3,580 
• Modelled Residue Count: 386 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable GTP-binding protein engB	A, B	195	Thermotoga maritima	Mutation(s): 0  Gene Names: engB, TM_1466
UniProt
Find proteins for Q9X1H7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H7  Go to UniProtKB:  Q9X1H7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PEG	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 62.67	α = 90
b = 69.714	β = 90
c = 94.836	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Chan, K.H., Wong, K.B.

Revision History  

• 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