9QUM | pdb_00009qum

Structure of lysozyme by continuous serial electron diffraction (SerialED)

PDB DOI: https://doi.org/10.2210/pdb9QUM/pdb

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

Deposited: 2025-04-10 Released: 2026-04-22
Deposition Author(s): Hofer, G., Wang, L., Pacoste, L., Hager, P., Fonjallaz, A., Scaletti Hutchinson, E., Stenmark, P., Di Palma, M., Williams, L., Worral, J., Steiner, R., Xu, H., Zou, X.
Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 0.83 Å
R-Value Free:
0.206 (Depositor), 0.228 (DCC)
R-Value Work:
0.175 (Depositor), 0.209 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Continuous Serial Electron Diffraction for High Quality Protein Structures

Hofer, G., Wang, L., Pacoste, L., Hager, P., Fonjallaz, A., Williams, L., Worrall, J., Steiner, R., Xu, H., Zou, X.

To be published.

Macromolecule Content

Total Structure Weight: 16.42 kDa
Atom Count: 1,200
Modeled Residue Count: 129
Deposited Residue Count: 147
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	147	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 0.83 Å
R-Value Free: 0.206 (Depositor), 0.228 (DCC)
R-Value Work: 0.175 (Depositor), 0.209 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.66	α = 87.73
b = 31.15	β = 108.97
c = 33.57	γ = 111.6

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-22

Deposition Author(s):

Scaletti Hutchinson, E.

Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	--
Swedish Research Council	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2026-04-22
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.