1I20 | pdb_00001i20

MUTANT HUMAN LYSOZYME (A92D)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 
    0.164 (Depositor) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Structural and thermodynamic responses of mutations at a Ca2+ binding site engineered into human lysozyme.

Kuroki, R.Yutani, K.

(1998) J Biological Chem 273: 34310-34315

  • DOI: https://doi.org/10.1074/jbc.273.51.34310
  • Primary Citation Related Structures: 
    1I1Z, 1I20, 1I22

  • PubMed Abstract: 

    Structural determinants of Ca2+ binding sites within proteins typically comprise several acidic residues in appropriate juxtaposition. Three residues (Ala-83, Gln-86, and Ala-92) in human lysozyme are characteristically mutated to Lys, Asp, and Asp, respectively, in natural Ca2+ binding lysozymes and alpha-lactalbumins. The effects of these mutations on the stability and Ca2+ binding properties of human lysozyme were investigated using calorimetry and were interpreted with crystal structures. The double mutant, in which Glu-86 and Ala-92 were replaced with Asp, clearly showed Ca2+ binding affinity, whereas neither point mutant showed Ca2+ affinity, indicating that both residues are essential. The further mutation of Ala-83 --> Lys did not affect the Ca2+ binding of the double mutant. The point mutations Ala-83 --> Lys and Glu-86 --> Asp did not affect the stability, whereas the mutation Ala-92 --> Asp was about 1.3 kcal/mol less stable. Structural analyses showed that both Asp-86 and Lys-83 were exposed to solvent. Side chains of Asp-86 and Asp-91 were rotated in opposite directions about chi1 angle, as if to reduce the electrostatic repulsion. The charged amino acids at the Ca2+ binding site did not significantly affect stability of the protein, possibly because of the local conformational change of the side chains.


  • Organizational Affiliation
    • Central Laboratories for Key Technology, Kirin Brewery Co. Ltd., 1-13-5 Fukuura, Kanazawa-ku, Yokohama 236 Japan. r-kuroki@kirin.co.jp

Macromolecule Content 

  • Total Structure Weight: 14.76 kDa 
  • Atom Count: 1,114 
  • Modeled Residue Count: 130 
  • Deposited Residue Count: 130 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LYSOZYME C130Homo sapiensMutation(s): 1 
EC: 3.2.2.17 (PDB Primary Data), 3.2.1.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens)
Explore P61626 
Go to UniProtKB:  P61626
PHAROS:  P61626
GTEx:  ENSG00000090382 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61626
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work:  0.164 (Depositor) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.07α = 90
b = 60.63β = 90
c = 33.85γ = 90
Software Package:
Software NamePurpose
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2001-02-28 
  • Deposition Author(s): Kuroki, R.

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary