6TTD | pdb_00006ttd

Crystal structure of McoA multicopper oxidase 2F4 variant from the hyperthermophile Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb6TTD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-12-26 Released: 2021-04-07
Deposition Author(s): Borges, P.T., Brissos, V., Cordeiro, T.N., Martins, L.O., Frazao, C.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia, Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.160 (Depositor), 0.155 (DCC)
R-Value Work:
0.160 (Depositor), 0.153 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Distal Mutations Shape Substrate-Binding Sites during Evolution of a Metallo-Oxidase into a Laccase

Brissos, V., Borges, P.T., Nunez-Franco, R., Lucas, M.F., Frazao, C., Monza, E., Masgrau, L., Cordeiro, T.N., Martins, L.O.

(2022) ACS Catal

DOI: https://doi.org/10.1021/acscatal.2c00336

Macromolecule Content

Total Structure Weight: 119.91 kDa
Atom Count: 8,220
Modeled Residue Count: 914
Deposited Residue Count: 1,054
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multicopper oxidase	A, B	527	Aquifex aeolicus	Mutation(s): 0 Gene Names: sufI, aq_1130
UniProt
Find proteins for O67206 (Aquifex aeolicus (strain VF5)) Explore O67206 Go to UniProtKB: O67206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67206
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	H [auth A], I [auth A], J [auth A], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B]	K [auth A], L [auth A], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] M [auth B] C [auth A], D [auth A], E [auth A], F [auth A], M [auth B], N [auth B], O [auth B], P [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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B]	G [auth A], Q [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.160 (Depositor), 0.155 (DCC)
R-Value Work: 0.160 (Depositor), 0.153 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.2	α = 90
b = 89.58	β = 106.07
c = 86.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
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: 2021-04-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BBBEBB/0122/2014
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BII-BBF/29564/2017
Other government	Portugal	LISBOA-01-0145-FEDER-007660

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2021-12-22
Changes: Database references, Experimental preparation
Version 1.2: 2022-04-27
Changes: Database references
Version 1.3: 2024-01-24
Changes: Data collection, Refinement description