1IO5

HYDROGEN AND HYDRATION OF HEN EGG-WHITE LYSOZYME DETERMINED BY NEUTRON DIFFRACTION

• PDB DOI: https://doi.org/10.2210/pdb1IO5/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2001-01-14 Released: 2001-02-07 
• Deposition Author(s): Niimura, N., Minezaki, Y., Nonaka, T., Castagna, J.C., Cipriani, F., Hoeghoej, P., Lehmann, M.S., Wilkinson, C.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.323 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.

Niimura, N., Minezaki, Y., Nonaka, T., Castagna, J.C., Cipriani, F., Hoghoj, P., Lehmann, M.S., Wilkinson, C.

(1997) Nat Struct Biol 4: 909-914

• PubMed: 9360606 
• DOI: https://doi.org/10.1038/nsb1197-909
• Primary Citation of Related Structures:  
  1IO5


• PubMed Abstract: 
  

  Neutron quasi-Laue diffraction data (2 A resolution) from tetragonal hen egg-white lysozyme were collected in ten days with neutron imaging plates. The data processing Laue software, LAUEGEN, developed for X-ray Laue diffractometry, was adapted for neutron diffractometry with a cylindrical detector. The data analysis software, X-PLOR, was modified and used for the refinement of hydrogen atoms, and the positions of 960 hydrogen atoms in the protein and 157 bound water molecules, were determined. Several examples are given of the methods used to identify hydrogen atoms and water molecules.

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Organizational Affiliation: 

Advanced Science Research Center, Japan Atomic Energy Research Institute, Tokai-mura, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.33 kDa 
• Atom Count: 1,252 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.323 
• R-Value Observed: 0.210 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.8	α = 90
b = 80.8	β = 90
c = 37.1	γ = 90

Software Package:

Software Name	Purpose
CCP4	refinement
INTLDM	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data reduction
INTLDM	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-07 
Deposition Author(s): Niimura, N., Minezaki, Y., Nonaka, T., Castagna, J.C., Cipriani, F., Hoeghoej, P., Lehmann, M.S., Wilkinson, C.

Revision History  

• Version 1.0: 2001-02-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-03-07
  Changes: Data collection
• Version 1.5: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-10-16
  Changes: Structure summary