6JOW | pdb_00006jow

Exo-beta-D-glucosaminidase from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb6JOW/pdb

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


• Deposited: 2019-03-24 Released: 2020-03-25 
• Deposition Author(s): Mine, S., Watanabe, M.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.220 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Exo-beta-D-glucosaminidase from Pyrococcus furiosus

Mine, S., Watanabe, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 357.74 kDa 
• Atom Count: 27,343 
• Modeled Residue Count: 3,048 
• Deposited Residue Count: 3,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	762	Pyrococcus furiosus	Mutation(s): 0  Gene Names: PF0363
UniProt
Find proteins for Q8U3U2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3U2  Go to UniProtKB:  Q8U3U2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], L [auth C], M [auth D], N [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	E [auth A], K [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.220 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.13	α = 90
b = 149.597	β = 102.07
c = 147.315	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	model building
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Mine, S., Watanabe, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25450143

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description