5ANH | pdb_00005anh

CRYSTAL STRUCTURE OF LACCASE FROM BASIDIOMYCETE PM1 (CECT 2971)

PDB DOI: https://doi.org/10.2210/pdb5ANH/pdb

Classification: OXIDOREDUCTASE
Organism(s): basidiomycete PM1
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2015-09-07 Released: 2016-08-24
Deposition Author(s): Medrano, F.J., Romero, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.273 (Depositor), 0.275 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Re-Designing the Substrate Binding Pocket of Laccase for Enhanced Oxidation of Sinapic Acid

Pardo, I., Santiago, G., Gentili, P., Lucas, F., Monza, E., Medrano, F.J., Romero, A., Galli, C., Martinez, A.T., Guallar, V., Camarero, S.

(2016) Catal Sci Technol 6: 3900

DOI: https://doi.org/10.1039/C5CY01725D

Macromolecule Content

Total Structure Weight: 161.07 kDa
Atom Count: 11,869
Modeled Residue Count: 1,488
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LACCASE	A, B, C	496	basidiomycete PM1	Mutation(s): 0 EC: 1.10.3.2
UniProt
Find proteins for Q12571 (basidiomycete PM1) Explore Q12571 Go to UniProtKB: Q12571
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12571
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.273 (Depositor), 0.275 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.44	α = 90
b = 175.66	β = 104.16
c = 103.7	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-24

Deposition Author(s):

Medrano, F.J.

Romero, A.

Revision History (Full details and data files)

Version 1.0: 2016-08-24
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary