4DWW

Crystal Structure of Nattokinase from Bacillus subtilis natto


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.133 

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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 66: 1670-1673

  • DOI: 10.1107/S1744309110043137

  • 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. ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subtilisin NAT
A
275Bacillus subtilis subsp. nattoMutation(s): 0 
Gene Names: aprN
EC: 3.4.21.62
Find proteins for P35835 (Bacillus subtilis subsp. natto)
Go to UniProtKB:  P35835
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEB
Query on SEB
A
L-PEPTIDE LINKINGC10 H13 N O5 SSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.133 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.293α = 90.00
b = 49.899β = 95.24
c = 56.338γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release