Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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Refined structure of the chitinase from barley seeds at 2.0 a resolution.

Song, H.K.Suh, S.W.

(1996) Acta Crystallogr D Biol Crystallogr 52: 289-298

  • DOI: https://doi.org/10.1107/S0907444995009061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Chitinase from barley seeds is a monomeric enzyme with 243 amino-acid residues and it plays a role as a defense protein. Its structure, previously determined at 2.8 A resolution by multiple isomorphous replacement method, is mainly alpha-helical [Hart, Monzingo, Ready, Ernst & Robertus, (1993). J. Mol. Biol. 229, 189-193]. The crystallization and preliminary X-ray data of the same enzyme in a different crystal form has been reported independently [Song, Hwang, Kim & Suh, (1993). Proteins, 17, 107-109}, the asymmetric unit of which contains two chitinase molecules. As a step toward understanding the general principles of catalysis, reported here is the structure of chitinase from barley seeds in this crystal form, as determined by molecular replacement and subsequently refined at 2.0 A resolution, with incorporation of partial data to 1.9 A (R factor of 18.9% for 31 038 unique reflections with F(o)> 2sigma(F) in the range 8.0-1.9 A). The r.m.s. deviations from ideal stereochemistry are 0.013 A for bond lengths and 1.32 degrees for bond angles. A superposition of the two independent molecules in the asymmetric unit gives an r.m.s. difference of 0.55 A for all protein atoms (0.43 and 0.74 A for main-chain and side-chain atoms, respectively). When the refined model of each chitinase molecule in the asymmetric unit is superposed with the starting model, the r.m.s. difference for all shared protein atoms is 0.99 A for molecule 1 and 0.85 A for molecule 2, respectively. Through a sequence comparison with homologous plant chitinases as well as a structural comparison with the active sites of other glycosidases, key catalytic residues have been identified and the active site has been located in the three-dimensional structure of the barley chitinase. The present structure, refined at an effective resolution of 2.0 A with incorporation of partial data to 1.9 A, represents a significant improvement in resolution compared to the previously reported model. The improved resolution has enabled the location of solvent atoms, including water molecules near the catalytic residues, in addition to the positioning of protein atoms with greater accuracy.

  • Organizational Affiliation

    Department of Chemistry and Center for Molecular Caralysis, Seoul National University, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
243Hordeum vulgareMutation(s): 0 
Find proteins for P23951 (Hordeum vulgare)
Explore P23951 
Go to UniProtKB:  P23951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23951
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.38α = 90
b = 44.47β = 111.99
c = 81.49γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
X-PLORmodel building
MADNESdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance