2ZIJ

Crystal Structure of Human Lysozyme Expressed in E. coli.

• PDB DOI: https://doi.org/10.2210/pdb2ZIJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-18 Released: 2009-01-06 
• Deposition Author(s): Tamada, T., Kuroki, R., Koshiba, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.167 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Preparation and characterization of methyonyl-lysine attached human lysozyme expressed in Escherichia coli and its effective conversion to the authentic-like protein

Shoyama, Y., Tamada, T., Nitta, K., Kumagai, I., Kuroki, R., Koshiba, T.

To be published.

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: 14.74 kDa 
• Atom Count: 1,161 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	130	Homo sapiens	Mutation(s): 0  Gene Names: LYZ, LZM EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens) Explore P61626  Go to UniProtKB:  P61626
PHAROS:  P61626 GTEx:  ENSG00000090382

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.167 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.6	α = 90
b = 61	β = 90
c = 33.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Tamada, T., Kuroki, R., Koshiba, T.

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary