3QPK | pdb_00003qpk

Probing oxygen channels in Melanocarpus albomyces laccase

PDB DOI: https://doi.org/10.2210/pdb3QPK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Melanocarpus albomyces
Expression System: Trichoderma reesei
Mutation(s): No

Deposited: 2011-02-14 Released: 2011-05-11
Deposition Author(s): Kallio, J.P., Rouvinen, J., Hakulinen, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.270 (Depositor), 0.268 (DCC)
R-Value Work:
0.214 (Depositor), 0.212 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Probing the Dioxygen Route in Melanocarpus albomyces Laccase with Pressurized Xenon Gas.

Kallio, J.P., Rouvinen, J., Kruus, K., Hakulinen, N.

(2011) Biochemistry 50: 4396-4398

PubMed: 21524088 Search on PubMed
DOI: https://doi.org/10.1021/bi200486b
Primary Citation Related Structures:
3QPK

PubMed Abstract:
Laccases catalyze the oxidation of phenolic substrates and the concominant reduction of dioxygen to water. We used xenon as an oxygen probe in search of routes for the entry of dioxygen into the catalytic center. Two xenon-pressurized crystal structures of recombinant Melanocarpus albomyces laccase were determined, showing three hydrophobic Xe-binding sites located in domain C. The analysis of hydrophobic cavities in other laccase structures further suggested the preference of domain C for binding of hydrophobic species such as dioxygen, thus suggesting that the hydrophobic core of domain C could function as a channel through which dioxygen can enter the trinuclear copper center.

Organizational Affiliation

Department of Chemistry, University of Eastern Finland, Joensuu, Finland.

Macromolecule Content

Total Structure Weight: 129.33 kDa
Atom Count: 10,254
Modeled Residue Count: 1,118
Deposited Residue Count: 1,118
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase-1	A, B	559	Melanocarpus albomyces	Mutation(s): 0 Gene Names: LAC1 EC: 1.10.3.2
UniProt
Find proteins for Q70KY3 (Melanocarpus albomyces) Explore Q70KY3 Go to UniProtKB: Q70KY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q70KY3
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G C, D, E, F, G, H, I	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	AA [auth B], BA [auth B], CA [auth B], O [auth A], P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain O [auth A] Focus chain P [auth A]
XE Query on XE Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	DA [auth B] EA [auth B] FA [auth B] Q [auth A] R [auth A] DA [auth B], EA [auth B], FA [auth B], Q [auth A], R [auth A], S [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	T [auth A], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain T [auth A] Focus chain U [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] V [auth B] J [auth A], K [auth A], L [auth A], M [auth A], V [auth B], W [auth B], X [auth B], Y [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Z [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Z [auth B]	N [auth A], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain Z [auth B] Interactions & Density Focus chain N [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.270 (Depositor), 0.268 (DCC)
R-Value Work: 0.214 (Depositor), 0.212 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.15	α = 90
b = 60.2	β = 99.79
c = 114.44	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-05-11

Deposition Author(s):

Kallio, J.P.

Rouvinen, J.

Hakulinen, N.

Revision History (Full details and data files)

Version 1.0: 2011-05-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary