6SYY | pdb_00006syy

Crystal structure of McoA multicopper oxidase from the hyperthermophile Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb6SYY/pdb

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


• Deposited: 2019-10-01 Released: 2020-06-17 
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

The Methionine-Rich Loop of Multicopper Oxidase McoA follows Open-To-Close Transitions with a Role in Enzyme Catalysis

Borges, P.T., Brissos, V., Cordeiro, T.N., Martins, L.O., Frazao, C.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c01623

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.82 kDa 
• Atom Count: 3,948 
• Modeled Residue Count: 456 
• Deposited Residue Count: 527 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic cell division protein (SufI)	A	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
O (Subject of Investigation/LOI)	F [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.92	α = 90
b = 98.927	β = 90
c = 98.589	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Borges, P.T., Brissos, V., Cordeiro, T.N., Martins, L.O., Frazao, C.

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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  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2021-06-30
  Changes: Data collection
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description