2HYK

The crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96

• PDB DOI: https://doi.org/10.2210/pdb2HYK/pdb

• Classification: HYDROLASE
• Organism(s): Nocardiopsis sp. F96
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-07 Released: 2007-10-02 
• Deposition Author(s): Fibriansah, G., Nakamura, S., Kumasaka, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.162 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

Literature

The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.

Fibriansah, G., Masuda, S., Koizumi, N., Nakamura, S., Kumasaka, T.

(2007) Proteins 69: 683-690

• PubMed: 17879342 
• DOI: https://doi.org/10.1002/prot.21589
• Primary Citation of Related Structures:  
  2HYK

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Organizational Affiliation: 

Department of Life Science, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.63 kDa 
• Atom Count: 2,140 
• Modelled Residue Count: 237 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,3-glucanase	A	245	Nocardiopsis sp. F96	Mutation(s): 0  EC: 3.2.1.39
UniProt
Find proteins for Q2V0H0 (Nocardiopsis sp. F96) Explore Q2V0H0  Go to UniProtKB:  Q2V0H0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EOH	D [auth A], E [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.162 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.589	α = 90
b = 71.843	β = 90.21
c = 39.666	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Fibriansah, G., Nakamura, S., Kumasaka, T.

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations