7CDR

Lysozyme room-temperature structure determined by SS-ROX combined with HAG method, 210 kGy (3000 images)

• PDB DOI: https://doi.org/10.2210/pdb7CDR/pdb

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


• Deposited: 2020-06-20 Released: 2021-03-10 
• Deposition Author(s): Hasegawa, K., Baba, S., Kawamura, T., Yamamoto, M., Kumasaka, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method.

Hasegawa, K., Baba, S., Kawamura, T., Yamamoto, M., Kumasaka, T.

(2021) Acta Crystallogr D Biol Crystallogr 77: 300-312

• DOI: https://doi.org/10.1107/S2059798321001686

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: 14.46 kDa 
• Atom Count: 1,058 
• 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  Gene Names: LYZ 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
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.372	α = 90
b = 78.372	β = 90
c = 38.68	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Hasegawa, K., Baba, S., Kawamura, T., Yamamoto, M., Kumasaka, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101070
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05783

Revision History  

• Version 1.0: 2021-03-10
  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