3FE0

X-ray crystal structure of wild type human lysozyme in D2O

• PDB DOI: https://doi.org/10.2210/pdb3FE0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2008-11-27 Released: 2009-12-08 
• Deposition Author(s): Chiba-Kamoshida, K., Matsui, T., Chatake, T., Ohhara, T., Ostermann, A., Tanaka, I., Yutani, K., Niimura, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.206 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Site-specific softening of peptide bonds by localized deuterium observed by neutron crystallography of human lysozyme hydrogen

Chiba-Kamoshida, K., Matsui, T., Chatake, T., Ohhara, T., Ostermann, A., Tanaka, I., Yutani, K., Niimura, N.

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: 14.72 kDa 
• Atom Count: 1,167 
• 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  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.206 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.170 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.825	α = 90
b = 56.883	β = 90
c = 60.965	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Chiba-Kamoshida, K., Matsui, T., Chatake, T., Ohhara, T., Ostermann, A., Tanaka, I., Yutani, K., Niimura, N.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary