5NE0 | pdb_00005ne0

Room temperature in-situ structure of hen egg-white lysozyme from crystals enclosed between ultrathin silicon nitride membranes

• PDB DOI: https://doi.org/10.2210/pdb5NE0/pdb

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


• Deposited: 2017-03-09 Released: 2017-06-14 
• Deposition Author(s): Martiel, I., Opara, N., Arnold, S.A., Braun, T., Stahlberg, H., Makita, M., David, C., Padeste, C.
• Funding Organization(s): Swiss Nanoscience Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.184 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free-electron lasers.

Opara, N., Martiel, I., Arnold, S.A., Braun, T., Stahlberg, H., Makita, M., David, C., Padeste, C.

(2017) J Appl Crystallogr 50: 909-918

• DOI: https://doi.org/10.1107/S1600576717005799

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: 1,092 
• Modeled 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	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.184 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.5	α = 90
b = 79.5	β = 90
c = 37.81	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Martiel, I., Opara, N., Arnold, S.A., Braun, T., Stahlberg, H., Makita, M., David, C., Padeste, C.

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Funding Organization	Location	Grant Number
Swiss Nanoscience Institute	Switzerland	P1305

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary