4X4K | pdb_00004x4k

Structure of laccase from Botrytis aclada with full copper content

PDB DOI: https://doi.org/10.2210/pdb4X4K/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Botrytis aclada
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2014-12-03 Released: 2015-12-09
Deposition Author(s): Osipov, E.M., Polyakov, K.M., Tikhonova, T.V., Kittl, R., Shleev, S.V., Ludwig, R., Popov, V.O.
Funding Organization(s): Russian Foundation for Basic Research, Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.233 (Depositor), 0.232 (DCC)
R-Value Work:
0.181 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Literature

Incorporation of copper ions into crystals of T2 copper-depleted laccase from Botrytis aclada.

Osipov, E.M., Polyakov, K.M., Tikhonova, T.V., Kittl, R., Dorovatovskii, P.V., Shleev, S.V., Popov, V.O., Ludwig, R.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1465-1469

PubMed: 26625287 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X1502052X
Primary Citation Related Structures:
4X4K

PubMed Abstract:
Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase from Botrytis aclada has been solved previously. With the aim of obtaining the structure of the native form of the enzyme, crystals of the depleted laccase were soaked in Cu(+)- and Cu(2+)-containing solutions. Copper ions were found to be incorporated into the active site only when Cu(+) was used. A comparative analysis of the native and depleted forms of the enzymes was performed.

Organizational Affiliation

Laboratory of Enzyme Engineering, A. N. Bach Institute of Biochemistry, Leninsky pr. 33, Moscow 119071, Russian Federation.

Macromolecule Content

Total Structure Weight: 67.03 kDa
Atom Count: 4,444
Modeled Residue Count: 525
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase	A	580	Botrytis aclada	Mutation(s): 0 EC: 1.10.3.2
UniProt
Find proteins for H8ZRU2 (Botrytis aclada) Explore H8ZRU2 Go to UniProtKB: H8ZRU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H8ZRU2
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G02763QD GlyCosmos: G02763QD GlyGen: G02763QD

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain H [auth A] 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 H [auth A] 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 H [auth A] 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], H [auth A]	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 H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.233 (Depositor), 0.232 (DCC)
R-Value Work: 0.181 (Depositor), 0.182 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.4	α = 90
b = 113.1	β = 109
c = 79.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	13-04-12083
Austrian Science Fund	Austria	P25148-B20

Revision History (Full details and data files)

Version 1.0: 2015-12-09
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary