4DWW

Crystal Structure of Nattokinase from Bacillus subtilis natto

• PDB DOI: https://doi.org/10.2210/pdb4DWW/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. natto
• Mutation(s): No 


• Deposited: 2012-02-27 Released: 2012-03-14 
• Deposition Author(s): Chatake, T., Yanagisawa, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

Yanagisawa, Y., Chatake, T., Chiba-Kamoshida, K., Naito, S., Ohsugi, T., Sumi, H., Yasuda, I., Morimoto, Y.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1670-1673

• PubMed: 21139221 
• DOI: https://doi.org/10.1107/S1744309110043137
• Primary Citation of Related Structures:  
  4DWW


• PubMed Abstract: 
  

  Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, β=95.2°. Diffraction images were processed to a resolution of 1.74 Å with an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba 288-0025, Japan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 27.98 kDa 
• Atom Count: 2,308 
• Modelled Residue Count: 275 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin NAT	A	275	Bacillus subtilis subsp. natto	Mutation(s): 0  EC: 3.4.21.62
UniProt
Find proteins for P35835 (Bacillus subtilis subsp. natto) Explore P35835  Go to UniProtKB:  P35835

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEB	A	L-PEPTIDE LINKING	C10 H13 N O5 S		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.293	α = 90
b = 49.899	β = 95.24
c = 56.338	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Chatake, T., Yanagisawa, Y.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description