7D01

Lysozyme structure SS2 from SS mode

• PDB DOI: https://doi.org/10.2210/pdb7D01/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-09 Released: 2021-03-31 
• Deposition Author(s): Kang, H.S., Lee, S.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

High-brightness self-seeded X-ray free-electron laser covering the 3.5 keV to 14.6 keV range

Nam, I., Min, C.K., Oh, B., Kim, G., Na, D., Suh, Y.J., Yang, H., Cho, M.H., Kim, C., Kim, M.J., Shim, C.H., Ko, J.H., Heo, H., Park, J., Kim, J., Park, S., Park, G., Kim, S., Chun, S.H., Hyun, H., Lee, J.H., Kim, K.S., Eom, I., Rah, S., Shu, D., Kim, K.J., Terentyev, S., Blank, V., Shvydko, Y., Lee, S.J., Kang, H.S.

(2021) Nat Photonics 

• DOI: https://doi.org/10.1038/s41566-021-00777-z

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.26 kDa 
• Atom Count: 1,094 
• Modelled Residue Count: 129 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	147	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.86	α = 90
b = 78.86	β = 90
c = 37.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Kang, H.S., Lee, S.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2017R1A2B4007274
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1F1A1075828
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1A6B4023605

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary