4JSO

The X-ray crystal structure of a thermophilic cellobiose binding protein bound with laminaripentaose

• PDB DOI: https://doi.org/10.2210/pdb4JSO/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-03-22 Released: 2013-10-09 
• Deposition Author(s): Munshi, P., Cuneo, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Molecular details of ligand selectivity determinants in a promiscuous beta-glucan periplasmic binding protein.

Munshi, P., Stanley, C.B., Ghimire-Rijal, S., Lu, X., Myles, D.A., Cuneo, M.J.

(2013) BMC Struct Biol 13: 18-18

• PubMed: 24090243 
• DOI: https://doi.org/10.1186/1472-6807-13-18
• Primary Citation of Related Structures:  
  4JSD, 4JSO


• PubMed Abstract: 
  

  Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively.

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Organizational Affiliation: 

Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 68.28 kDa 
• Atom Count: 5,127 
• Modelled Residue Count: 582 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein	A	582	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM0031, TM_0031
UniProt
Find proteins for Q9WXN8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXN8  Go to UniProtKB:  Q9WXN8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G03330ED GlyCosmos:  G03330ED

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.922	α = 90
b = 89.785	β = 90
c = 108.321	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Munshi, P., Cuneo, M.J.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary