7YRK | pdb_00007yrk

Crystal structure of the hen egg lysozyme-2-oxidobenzylidene-threoninato-copper (II) complex

PDB DOI: https://doi.org/10.2210/pdb7YRK/pdb

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

Deposited: 2022-08-10 Released: 2023-05-10
Deposition Author(s): Unno, M., Furuya, T., Kitanishi, K., Akitsu, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free:
0.128 (Depositor), 0.126 (DCC)
R-Value Work:
0.113 (Depositor), 0.111 (DCC)
R-Value Observed:
0.114 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme.

Furuya, T., Nakane, D., Kitanishi, K., Katsuumi, N., Tsaturyan, A., Shcherbakov, I.N., Unno, M., Akitsu, T.

(2023) Sci Rep 13: 6892-6892

PubMed: 37106030 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-023-33926-1
Primary Citation of Related Structures:
7YRK

PubMed Abstract:
A novel hybrid protein composed of a superoxide dismutase-active Cu(II) complex (CuST) and lysozyme (CuST@lysozyme) was prepared. The results of the spectroscopic and electrochemical analyses confirmed that CuST binds to lysozyme. We determined the crystal structure of CuST@lysozyme at 0.92 Å resolution, which revealed that the His15 imidazole group of lysozyme binds to the Cu(II) center of CuST in the equatorial position. In addition, CuST was fixed in position by the weak axial coordination of the Thr89 hydroxyl group and the hydrogen bond between the guanidinium group of the Arg14 residue and the hydroxyl group of CuST. Furthermore, the combination of CuST with lysozyme did not decrease the superoxide dismutase activity of CuST. Based on the spectral, electrochemical, structural studies, and quantum chemical calculations, an O ₂ ^- disproportionation mechanism catalyzed by CuST@lysozyme is proposed.

Organizational Affiliation

Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.

Macromolecule Content

Total Structure Weight: 16.89 kDa
Atom Count: 1,400
Modelled Residue Count: 129
Deposited Residue Count: 147
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JI6 (Subject of Investigation/LOI) Query on JI6 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(6~{S})-6-[(1~{R})-1-oxidanylethyl]-2,4-dioxa-7$l^{4}-aza-3$l^{3}-cupratricyclo[7.4.0.0^{3,7}]trideca-1(13),7,9,11-tetraen-5-one C₁₁ H₁₁ Cu N O₄ RLMUPHKMYNMLMB-NBDMYRNNSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain H [auth A] mmCIF format, chain B [auth A] mmCIF format, chain H [auth A]	B [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	A	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free: 0.128 (Depositor), 0.126 (DCC)
R-Value Work: 0.113 (Depositor), 0.111 (DCC)
R-Value Observed: 0.114 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.671	α = 90
b = 78.671	β = 90
c = 37.203	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H00336

Revision History (Full details and data files)

Version 1.0: 2023-05-10
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 2.0: 2024-09-25
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary