1JEF

TURKEY LYSOZYME COMPLEX WITH (GLCNAC)3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report



Literature

X-ray structure of turkey-egg lysozyme complex with tri-N-acetylchitotriose. Lack of binding ability at subsite A.

Harata, K.Muraki, M.

(1997) Acta Crystallogr D Biol Crystallogr 53: 650-657

  • DOI: 10.1107/S0907444997005362
  • Primary Citation of Related Structures:  
    1JEF

  • PubMed Abstract: 
  • The turkey-egg lysozyme (TEL) complex with tri-N-acetylchitotriose [(GlcNac)3] was co-crystallized from 1.5% TEL and 2 mM (GlcNac)3 at pH 4.2. The crystal structure was determined by molecular replacement and refined to an R value of 0.182 using 10-1 ...

    The turkey-egg lysozyme (TEL) complex with tri-N-acetylchitotriose [(GlcNac)3] was co-crystallized from 1.5% TEL and 2 mM (GlcNac)3 at pH 4.2. The crystal structure was determined by molecular replacement and refined to an R value of 0.182 using 10-1.77 A data. The (GlcNac)3 molecule occupies the subsites A, B and C. At the subsites B and C, the sugar residues are bound in a similar manner to that found in the hen-egg lysozyme (HEL) complex. In contrast, the GlcNac residue at the subsite A is exposed to bulk solvent and has no contact with the protein molecule because the active residue Asp101 in HEL is replaced by Gly in TEL. A sulfate ion is bound in the vicinity of subsite B and forms hydrogen bonds with the sugar residue and the guanidino group of Arg61, assisting the binding of the sugar residue to subsite B. The active-site cleft of TEL is narrower than that of native TEL, thus attaining the best fit of the (GlcNac)3 molecule. The lack of binding ability of subsite A is discussed in relation to the catalytic properties of TEL. The result suggests that the cleavage pattern of oligosaccharide substrates in the catalytic reaction is regulated by the protein-sugar interaction at subsite A.


    Related Citations: 
    • X-Ray Structure of Turkey Egg Lysozyme Complex with Di-N-Acetylchitobiose. Recognition and Binding of Alpha-Anomeric Form
      Harata, K., Muraki, M.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 718
    • X-Ray Structure of Monoclinic Turkey Egg Lysozyme at 1.3 Angstrom Resolution
      Harata, K.
      (1993) Acta Crystallogr D Biol Crystallogr 49: 497

    Organizational Affiliation

    National Institute of Bioscience and Human Technology, Tsukuba, Ibaraki, Japan. harata@nibh.go.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA129Meleagris gallopavoMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00703 (Meleagris gallopavo)
Explore P00703 
Go to UniProtKB:  P00703
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
Btriacetyl-beta-chitotrioseOligosaccharide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.49α = 90
b = 32.94β = 119.1
c = 49γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
MERGEFdata reduction
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
MERGEFdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1997-04-23 
  • Released Date: 1997-10-15 
  • Deposition Author(s): Harata, K., Muraki, M.

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary