Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.33 kDa 
• Atom Count: 2511 
• Modelled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

1OM0

crystal structure of xylanase inhibitor protein (XIP-I) from wheat

• DOI: 10.2210/pdb1OM0/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Triticum aestivum
• Mutation(s): No 


• Deposited: 2003-02-24 Released: 2003-06-03 
• Deposition Author(s): Payan, F., Flatman, R., Porciero, S., Williamson, G., Juge, N., Roussel, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson).

Payan, F., Flatman, R., Porciero, S., Williamson, G., Juge, N., Roussel, A.

(2003) Biochem J 372: 399-405

• PubMed: 12617724 
• DOI: 10.1042/BJ20021802
• Primary Citation of Related Structures:  
  1OM0


• PubMed Abstract: 
  

A novel class of proteinaceous inhibitors exhibiting specificity towards microbial xylanases has recently been discovered in cereals. The three-dimensional structure of xylanase inhibitor protein I (XIP-I) from wheat (Triticum aestivum, var. Soisson) was determined by X-ray crystallography at 1.8 A (1 A=0.1 nm) resolution. The inhibitor possesses a (beta/alpha)(8) barrel fold and has structural features typical of glycoside hydrolase family 18, namely two consensus regions, approximately corresponding to the third and fourth barrel strands, and two non-proline cis -peptide bonds, Ser(36)-Phe and Trp(256)-Asp (in XIP-I numbering). However, detailed structural analysis of XIP-I revealed several differences in the region homologous with the active site of chitinases. The catalytic glutamic acid residue of family 18 chitinases [Glu(127) in hevamine, a chitinase/lysozyme from the rubber tree (Hevea brasiliensis)] is conserved in the structure of the inhibitor (Glu(128)), but its side chain is fully engaged in salt bridges with two neighbouring arginine residues. Gly(81), located in subsite -1 of hevamine, where the reaction intermediate is formed, is replaced by Tyr(80) in XIP-I. The tyrosine side chain fills the subsite area and makes a strong hydrogen bond with the side chain of Glu(190) located at the opposite side of the cleft, preventing access of the substrate to the catalytic glutamic acid. The structural differences in the inhibitor cleft structure probably account for the lack of activity of XIP-I towards chitin.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS and Universities Aix-Marseille I and II, 31 chemin Joseph Aiguier, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylanase Inhibitor Protein I	A	274	Triticum aestivum	Mutation(s): 0  Gene Names: XIPI
UniProt
Find proteins for Q8L5C6 (Triticum aestivum) Explore Q8L5C6  Go to UniProtKB:  Q8L5C6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.475	α = 90
b = 58.475	β = 90
c = 191.954	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2003-02-24 
• Released Date: 2003-06-03 
Deposition Author(s): Payan, F., Flatman, R., Porciero, S., Williamson, G., Juge, N., Roussel, A.

Revision History  

• Version 1.0: 2003-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary