Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.184 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a beta-sheet coil motif at 2.0 A resolution.

Hamada, K.Hata, Y.Katsuya, Y.Hiramatsu, H.Fujiwara, T.Katsube, Y.

(1996) J Biochem 119: 844-851

  • DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a021320
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of Serratia protease from Serratia sp. E-15 was solved by the single isomorphous replacement method supplemented with anomalous scattering effects from both the Zn atom in the native crystal and the Sm atom in the derivative crystal, and refined at 2.0 A resolution to a crystallographic R-factor of 0.194. The enzyme consists of N-terminal catalytic and C-terminal beta-sandwich domains, as observed in alkaline protease from Pseudomonas aeruginosa IFO3080. The catalytic domain with a five-stranded antiparallel beta-sheet and five alpha-helices shares a basically common folding topology with those of other zinc metalloendoproteases. The catalytic zinc ion at the bottom of the active site cleft is ligated by His176, His180, His186, Tyr216, and a water molecule in a distorted trigonalbipyramidal manner. The C-terminal domain is a beta-strand-rich domain containing eighteen beta-strands and a short alpha-helix, and has seven Ca2+ ions bound to calcium binding loops. An unusual beta-sheet coil motif is observed in this domain, where the beta-strands and calcium binding loops are alternately incorporated into an elliptical right-handed spiral so as to form a two-layer untwisted beta-sandwich structure. The Ca2+ ions in the C-terminal domain seem to be very important for the folding and stability of the beta-sheet coil structure.

  • Organizational Affiliation

    Faculty of Science, Shimane University. hamadak@cis.shimane.u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERRALYSIN471Serratia sp. E-15Mutation(s): 0 
Find proteins for P07268 (Serratia marcescens (strain ATCC 21074 / E-15))
Explore P07268 
Go to UniProtKB:  P07268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07268
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.184 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.14α = 90
b = 150.89β = 90
c = 42.64γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Other