6A10 | pdb_00006a10

Crystal structure of hen egg white lysozyme crystallized by ammonium sulfate

• PDB DOI: https://doi.org/10.2210/pdb6A10/pdb

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


• Deposited: 2018-06-06 Released: 2019-02-20 
• Deposition Author(s): Kitahara, M., Fudo, S., Yoneda, T., Nukaga, M., Hoshino, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Anisotropic Distribution of Ammonium Sulfate Ions in Protein Crystallization

Kitahara, M., Fudo, S., Yoneda, T., Nukaga, M., Hoshino, T.

(2019) Cryst Growth Des 19: 6004-6010

• DOI: https://doi.org/10.1021/acs.cgd.9b00256

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.95 kDa 
• Atom Count: 3,818 
• Modeled Residue Count: 387 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, B, C	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.399	α = 115.97
b = 57.971	β = 105.2
c = 57.618	γ = 98.81

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Kitahara, M., Fudo, S., Yoneda, T., Nukaga, M., Hoshino, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	15K08458

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 2.0: 2019-07-24
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-11-20
  Changes: Database references
• Version 2.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 2.3: 2024-11-20
  Changes: Structure summary