6K8G | pdb_00006k8g

H/D exchanged Hen egg-white lysozyme

• PDB DOI: https://doi.org/10.2210/pdb6K8G/pdb

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


• Deposited: 2019-06-11 Released: 2020-06-17 
• Deposition Author(s): Kita, A., Morimoto, Y.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.180 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.255 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state.

Kita, A., Morimoto, Y.

(2020) J Appl Crystallogr 53: 837-840

• PubMed: 32684898 
• DOI: https://doi.org/10.1107/S1600576720005488
• Primary Citation Related Structures: 
  6K8G


• PubMed Abstract: 
  

  Neutron diffraction studies of hydrogen/deuterium-exchanged hen egg-white lysozyme were performed by a joint X-ray and neutron refinement to elucidate the hydrogen/deuterium exchange behavior. Large crystals for neutron work, consisting of molecules that were exchanged before crystallization, were obtained by repeatedly adding protein solution to the crystal batch using deuterated precipitant reagent. There are differences in hydrogen/deuterium exchange behavior compared with previous crystallographic or NMR studies, which could be due to intermolecular interactions in the crystal or to different lengths of exchange period.

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Organizational Affiliation: 
• Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sen-nan, Osaka 590-0494, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.39 kDa 
• Atom Count: 1,086 
• Modeled 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.180 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.255 (Depositor) 
• R-Value Work:  0.225 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.094	α = 90
b = 79.094	β = 90
c = 37.828	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Kita, A., Morimoto, Y.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--
Other private	Japan	The Research Development Program of Kyoto University
Other private	Japan	The Towa Foundation for Food Science & Research

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2021-01-13
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary