2WBM

Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus

• PDB DOI: https://doi.org/10.2210/pdb2WBM/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-03-02 Released: 2009-06-02 
• Deposition Author(s): Ng, C.L., Isupov, M.N., Lebedev, A.A., Ortiz-Lombardia, M., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.214 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Literature

Conformational Flexibility and Molecular Interactions of an Archaeal Homologue of the Shwachman-Bodian-Diamond Syndrome Protein.

Ng, C.L., Waterman, D.G., Koonin, E.V., Walters, A.D., Chong, J.P., Isupov, M.N., Lebedev, A.A., Bunka, D.H., Stockley, P.G., Ortiz-Lombardia, M., Antson, A.A.

(2009) BMC Struct Biol 9: 32

• PubMed: 19454024 
• DOI: https://doi.org/10.1186/1472-6807-9-32
• Primary Citation of Related Structures:  
  2WBM


• PubMed Abstract: 
  

  Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown.

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Organizational Affiliation: 

York Structural Biology Laboratory, Chemistry Department, University of York, York, YO10 5YW, UK. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 57.63 kDa 
• Atom Count: 4,230 
• Modelled Residue Count: 461 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG	A, B	252	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0
UniProt
Find proteins for O26781 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26781  Go to UniProtKB:  O26781

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth B], J [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.214 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.3	α = 90
b = 72.108	β = 90
c = 146.829	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Ng, C.L., Isupov, M.N., Lebedev, A.A., Ortiz-Lombardia, M., Antson, A.A.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-03-07
  Changes: Source and taxonomy
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description