1NPC | pdb_00001npc

THE STRUCTURE OF NEUTRAL PROTEASE FROM BACILLUS CEREUS AT 0.2-NM RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1NPC/pdb

• Classification: HYDROLASE(METALLOPROTEINASE)
• Organism(s): Bacillus cereus
• Mutation(s): No 


• Deposited: 1992-01-08 Released: 1993-10-31 
• Deposition Author(s): Stark, W., Pauptit, R.A., Jansonius, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

The structure of neutral protease from Bacillus cereus at 0.2-nm resolution.

Stark, W., Pauptit, R.A., Wilson, K.S., Jansonius, J.N.

(1992) Eur J Biochem 207: 781-791

• PubMed: 1633827 
• DOI: https://doi.org/10.1111/j.1432-1033.1992.tb17109.x
• Primary Citation of Related Structures:  
  1NPC


• PubMed Abstract: 
  

  The crystal structure of the neutral protease from Bacillus cereus has been refined to an R factor of 17.5% at 0.2-nm resolution. The enzyme, an extracellular metalloendopeptidase, consists of two domains and binds one zinc and four calcium ions. The structure is very similar to that of thermolysin, with which the enzyme shares 73% amino-acid sequence identity. The active-site cleft between the two domains is wider in neutral protease than in thermolysin. This suggests the presence of a flexible hinge region between the two domains, which may assist enzyme action. The high-resolution analysis allows detailed examination of possible causes for the difference in thermostability between neutral protease and thermolysin.

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Organizational Affiliation: 

Department of Structural Biology, University of Basel, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.04 kDa 
• Atom Count: 2,699 
• Modelled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTRAL PROTEASE	A	317	Bacillus cereus	Mutation(s): 0  EC: 3.4.24.27 (PDB Primary Data), 3.4.24.28 (UniProt)
UniProt
Find proteins for P05806 (Bacillus cereus) Explore P05806  Go to UniProtKB:  P05806

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.5	α = 90
b = 76.5	β = 90
c = 201	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Stark, W., Pauptit, R.A., Jansonius, J.N.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations