9LMK | pdb_00009lmk

Room temperature structure of lysozyme by serial synchrotron crystallography (XDS)

• PDB DOI: https://doi.org/10.2210/pdb9LMK/pdb

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


• Deposited: 2025-01-19 Released: 2025-02-12 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Room temperature structure of lysozyme by serial synchrotron crystallography (XDS)

Nam, K.H.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,087 
• Modelled 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	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.18	α = 90
b = 79.18	β = 90
c = 38.35	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release