9GYH | pdb_00009gyh

HEW Lysozyme with His 15 functionalized with iodoacetamide

PDB DOI: https://doi.org/10.2210/pdb9GYH/pdb

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

Deposited: 2024-10-02 Released: 2025-02-26
Deposition Author(s): da Silva, J.S.P., Delgado, J.M.L., Bruno, F., Calderone, V., Ravera, E.
Funding Organization(s): Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of His15 acetamide-modified hen egg-white lysozyme: a nice surprise from an old friend.

Malanho da Silva, J., Lanuza, J., Bruno, F., Calderone, V., Ravera, E.

(2025) Acta Crystallogr F Struct Biol Commun 81: 41-46

PubMed: 39804568 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X2500010X
Primary Citation Related Structures:
9GYH

PubMed Abstract:
Hen egg-white lysozyme (HEWL) is a small polycationic protein which is highly soluble and stable. This has led to it becoming a `molecular laboratory' where chemical biological operations and structural techniques are tested. To date, HEWL accounts for 1233 PDB entries, roughly 0.5% of the total, making it the best-represented protein in the PDB. With the aim of unambiguously identifying the N atom of the His15 side chain that is most reactive towards iodoacetamide, the structure of chemically modified HEWL was determined by crystallizing it using the `15 minutes lysozyme' protocol. This protocol invariably yields tetragonal crystals of the unmodified protein. To our surprise, we found that the crystals of the modified protein had similar unit-cell parameters but that refinement was only possible when considering an orthorhombic system.

Organizational Affiliation

Department of Chemistry `Ugo Schiff', Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.

Macromolecule Content

Total Structure Weight: 29.1 kDa
Atom Count: 2,420
Modeled Residue Count: 258
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, B	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
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
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]