9RC3 | pdb_00009rc3

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 co-crystallized with Silver Nitrate

PDB DOI: https://doi.org/10.2210/pdb9RC3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pediococcus pentosaceus
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2025-05-27 Released: 2025-11-19
Deposition Author(s): Paredes, F., Casino, P.
Funding Organization(s): Generalitat Valenciana, Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.249 (Depositor), 0.253 (DCC)
R-Value Work:
0.202 (Depositor), 0.208 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Laccases from lactic acid bacteria show cuprous oxidase activity and capture Cu(II) and Ag(I) ions

Paredes, F., Casino, P.

(2025) Protein Sci

DOI: https://doi.org/10.1002/pro70385

Macromolecule Content

Total Structure Weight: 120.62 kDa
Atom Count: 7,347
Modeled Residue Count: 922
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multicopper oxidase, type 2	A, B	532	Pediococcus pentosaceus	Mutation(s): 0 EC: 1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG Query on AG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
CU Query on CU 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 F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [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 F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [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 F [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] F [auth A] I [auth B] C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [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 C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.249 (Depositor), 0.253 (DCC)
R-Value Work: 0.202 (Depositor), 0.208 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.122	α = 90
b = 121.122	β = 90
c = 174.556	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Paredes, F.

Casino, P.

Funding Organization	Location	Grant Number
Generalitat Valenciana	Spain	CIAICO/2022/142
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2019-110630GB-I00
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2022-141621NB-I00