9IG6 | pdb_00009ig6

Hen egg-white lysozyme structure determined by 3DED/MicroED on a 200 keV microscope

PDB DOI: https://doi.org/10.2210/pdb9IG6/pdb

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

Deposited: 2025-02-19 Released: 2025-03-19
Deposition Author(s): Shaikhqasem, A., Hamdi, F., Machner, L., Parthier, C., Breithaupt, C., Kyrilis, F.L., Feller, S.M., Kastritis, P.L., Stubbs, M.T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 2.80 Å
R-Value Free:
0.326 (Depositor), 0.360 (DCC)
R-Value Work:
0.294 (Depositor), 0.306 (DCC)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Hen egg-white lysozyme structure determined by 3DED/MicroED on a 200 keV microscope

Shaikhqasem, A., Hamdi, F., Machner, L., Parthier, C., Breithaupt, C., Kyrilis, F.L., Feller, S.M., Kastritis, P.L., Stubbs, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 14.33 kDa
Atom Count: 1,013
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 2.80 Å
R-Value Free: 0.326 (Depositor), 0.360 (DCC)
R-Value Work: 0.294 (Depositor), 0.306 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.59	α = 90
b = 78.59	β = 90
c = 37.84	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Shaikhqasem, A.

Kastritis, P.L.

Funding Organization	Location	Grant Number
Other government		BMBF ZIK HALOmem, grant no. 03Z22HN23
Other government		BMBF ZIK HALOmem, grant no. 03Z22HI2
Other government		BMBF, CORONAmem, grant no. 03COV04
Other government		EFRE for Saxony-Anhalt (grant no. ZS/2016/04/78115 and grant no. ZS/2024/05/187255
Other government		DFG, project numbers 391498659, RTG 2467 and 514901783, CRC 1664
Other government		The European Union Horizon Europe ERA Chair hot4cryo, project number 101086665

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.