3APG

Crystal structure of hyperthermophilic beta-glucosidase from pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb3APG/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-15 Released: 2011-10-19 
• Deposition Author(s): Kado, Y., Inoue, T., Ishikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.223 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Crystal structure of hyperthermophilic beta-glucosidase from pyrococcus furiosus

Kado, Y., Inoue, T., Ishikawa, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 219.68 kDa 
• Atom Count: 15,832 
• Modelled Residue Count: 1,884 
• Deposited Residue Count: 1,892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B, C, D	473	Pyrococcus furiosus	Mutation(s): 0  Gene Names: celB
UniProt
Find proteins for Q51723 (Pyrococcus furiosus) Explore Q51723  Go to UniProtKB:  Q51723

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth B], H [auth C], I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.223 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.962	α = 90
b = 141.962	β = 90
c = 343.013	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Kado, Y., Inoue, T., Ishikawa, K.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Refinement description
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations