2DSK

Crystal structure of catalytic domain of hyperthermophilic chitinase from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb2DSK/pdb

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


• Deposited: 2006-06-30 Released: 2007-02-06 
• Deposition Author(s): Nakamura, T., Mine, S., Hagihara, Y., Ishikawa, K., Uegaki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Structure of the catalytic domain of the hyperthermophilic chitinase from Pyrococcus furiosus

Nakamura, T., Mine, S., Hagihara, Y., Ishikawa, K., Uegaki, K.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 7-11

• PubMed: 17183162 
• DOI: https://doi.org/10.1107/S1744309106051773
• Primary Citation of Related Structures:  
  2DSK


• PubMed Abstract: 
  

  The crystal structure of the catalytic domain of a chitinase from the hyperthermophilic archaeon Pyrococcus furiosus (AD2(PF-ChiA)) has been determined at 1.5 A resolution. This is the first structure of the catalytic domain of an archaeal chitinase. The overall structure of AD2(PF-ChiA) is a TIM-barrel fold with a tunnel-like active site that is a common feature of family 18 chitinases. Although the catalytic residues (Asp522, Asp524 and Glu526) are conserved, comparison of the conserved residues and structures with those of other homologous chitinases indicates that the catalytic mechanism of PF-ChiA is different from that of family 18 chitinases.

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Organizational Affiliation: 

National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.18 kDa 
• Atom Count: 5,457 
• Modelled Residue Count: 600 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chitinase	A, B	311	Pyrococcus furiosus	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for Q8U1H5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1H5  Go to UniProtKB:  Q8U1H5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.959	α = 90
b = 92.78	β = 90
c = 107.228	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Nakamura, T., Mine, S., Hagihara, Y., Ishikawa, K., Uegaki, K.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations