2VRJ | pdb_00002vrj

Beta-glucosidase from Thermotoga maritima in complex with N-octyl-5- deoxy-6-oxa-N-(thio)carbamoylcalystegine

• PDB DOI: https://doi.org/10.2210/pdb2VRJ/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-04-09 Released: 2008-10-14 
• Deposition Author(s): Aguilar, M., Gloster, T.M., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Llebaria, A., Casas, J., Egido-Gabas, M., Garcia Fernandez, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis for Beta-Glucosidase Inhibition by Ring-Modified Calystegine Analogues.

Aguilar, M., Gloster, T.M., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Llebaria, A., Casas, J., Egido-Gabas, M., Garcia Fernandez, J.M.

(2008) Chembiochem 9: 2612

• PubMed: 18833549 
• DOI: https://doi.org/10.1002/cbic.200800451
• Primary Citation Related Structures: 
  2VRJ

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Organizational Affiliation: 
• Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Prof. García González 1, 41012 Sevilla, Spain.

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: 108.8 kDa 
• Atom Count: 8,070 
• Modeled Residue Count: 881 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE A	A, B	468	Thermotoga maritima	Mutation(s): 0  EC: 3.2.1.21
UniProt
Find proteins for Q08638 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q08638  Go to UniProtKB:  Q08638

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCW	C [auth A], G [auth B]	(1S,2R,3S,4R,5R)-2,3,4-trihydroxy-N-octyl-6-oxa-8-azabicyclo[3.2.1]octane-8-carbothioamide C15 H28 N2 O4 S LFSNQOFOMJLHIW-MEBFFEOJSA-N
ACT	E [auth A], F [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.696	α = 90
b = 94.409	β = 90
c = 113.026	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Aguilar, M., Gloster, T.M., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Llebaria, A., Casas, J., Egido-Gabas, M., Garcia Fernandez, J.M.

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description