5OR3 | pdb_00005or3

Crystal structure of Aspergillus oryzae catechol oxidase in met/deoxy-form

PDB DOI: https://doi.org/10.2210/pdb5OR3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus oryzae RIB40
Expression System: Trichoderma reesei RUT C-30
Mutation(s): No

Deposited: 2017-08-15 Released: 2018-05-09
Deposition Author(s): Hakulinen, N., Penttinen, L., Rutanen, C., Rouvinen, J.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.207 (Depositor), 0.198 (DCC)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

Penttinen, L., Rutanen, C., Saloheimo, M., Kruus, K., Rouvinen, J., Hakulinen, N.

(2018) PLoS One 13: e0196691-e0196691

PubMed: 29715329 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0196691
Primary Citation Related Structures:
5OR3, 5OR4

PubMed Abstract:
Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 174.91 kDa
Atom Count: 13,215
Modeled Residue Count: 1,485
Deposited Residue Count: 1,532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
catechol oxidase	A, B, C, D	383	Aspergillus oryzae RIB40	Mutation(s): 0 Gene Names: AO090001000383
UniProt
Find proteins for Q2UNF9 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2UNF9 Go to UniProtKB: Q2UNF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2UNF9
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	E, G	3		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	F	4		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain HA [auth C] SDF format, chain GA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C]	GA [auth C] HA [auth C] L [auth A] M [auth A] MA [auth D] GA [auth C], HA [auth C], L [auth A], M [auth A], MA [auth D], N [auth A], NA [auth D], OA [auth D], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain V [auth B] Focus chain W [auth B]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B]	X [auth B], Y [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain X [auth B] Focus chain Y [auth B]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain O [auth A] SDF format, chain LA [auth D] SDF format, chain K [auth A] SDF format, chain FA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth C]	FA [auth C], K [auth A], LA [auth D], O [auth A], U [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain FA [auth C] Focus chain K [auth A] Focus chain LA [auth D] Focus chain O [auth A] Focus chain U [auth B] Interactions & Density Focus chain FA [auth C] Focus chain K [auth A] Focus chain LA [auth D] Focus chain O [auth A] Focus chain U [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain EA [auth C] SDF format, chain DA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C]	DA [auth C] EA [auth C] I [auth A] J [auth A] JA [auth D] DA [auth C], EA [auth C], I [auth A], J [auth A], JA [auth D], KA [auth D], S [auth B], T [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain S [auth B] Focus chain T [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] P [auth A] Q [auth A] AA [auth B], BA [auth B], CA [auth B], P [auth A], Q [auth A], R [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Z [auth B]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] MOL2 format, chain IA [auth C] mmCIF format, chain IA [auth C]	IA [auth C]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Interactions & Density Focus chain IA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.207 (Depositor), 0.198 (DCC)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.627	α = 87.19
b = 81.392	β = 89.23
c = 82.2	γ = 73.89

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Academy of Finland	Finland	256937
Academy of Finland	Finland	292705

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary