Crystal structure of ICChI chitinase from ipomoea carnea

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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This is version 2.1 of the entry. See complete history


TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity.

Kumar, S.Kumar, A.Patel, A.K.

(2020) Phytochemistry 170: 112221-112221

  • DOI: https://doi.org/10.1016/j.phytochem.2019.112221
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The ICChI is a 35-kDa, glycosylated protein isolated from the latex of the weed Ipomoea carnea. It displays chitinase and lysozyme activity, which could be important for the defense against pathogenic fungi, insects and bacteria. The ICChI enzyme was crystallized, and a diffraction data set was collected from a single crystal to 1.42 Å resolution. The crystals belong to the primitive tetragonal space group P4 3 2 1 2, with unit-cell parameters a = b = 57.9, c = 172.0 Å, and α = β = γ = 90°. The structure was elucidated by molecular replacement method using a mixed model of three homologous structures from the N-terminal sequence of ICChI. The refined model consists of 272 amino acid residues and has a R factor of 18.93% and R free of 22.42%. The protein consists of a single globular domain with a (α/β) 8 triosephosphate isomerase barrel fold. Three of the consensus sites for N-glycosylation viz., Asn 45 , Asn 172 , and Asn 194 containing carbohydrate moieties N-Acetylglucosamine (NAG), mannose, fucose, and xylose. The putative catalytic residues are Asp 125 , Glu 127 , and Tyr 184 . The crystal structure may provide fundamental information of GH18 family chitinases.

  • Organizational Affiliation

    Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ICChI, a glycosylated chitinase272Ipomoea carneaMutation(s): 0 
Find proteins for A0A493R6X2 (Ipomoea carnea)
Explore A0A493R6X2 
Go to UniProtKB:  A0A493R6X2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A493R6X2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
B, C
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G68461PT
GlyCosmos:  G68461PT
GlyGen:  G68461PT
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.49α = 90
b = 59.49β = 90
c = 171.2γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary