8J6G | pdb_00008j6g

Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0

PDB DOI: https://doi.org/10.2210/pdb8J6G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arthrobacter globiformis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-25 Released: 2023-09-20
Deposition Author(s): Murakawa, T., Okajima, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free:
0.161 (Depositor), 0.161 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.225 (Depositor)
R-Value Work:
0.198 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor

Murakawa, T., Kurihara, K., Shoji, M., Yano, N., Kusaka, K., Kawano, Y., Suzuki, M., Shigeta, Y., Yano, T., Adachi, M., Tanizawa, K., Okajima, T.

(2023) ACS Catal : 12403-12413

DOI: https://doi.org/10.1021/acscatal.3c02629

Macromolecule Content

Total Structure Weight: 69.22 kDa
Atom Count: 6,379
Modeled Residue Count: 621
Deposited Residue Count: 621
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethylamine oxidase	A	621	Arthrobacter globiformis	Mutation(s): 0 EC: 1.4.3.21
UniProt
Find proteins for P46881 (Arthrobacter globiformis) Explore P46881 Go to UniProtKB: P46881
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEA (Subject of Investigation/LOI) Query on PEA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-PHENYLETHYLAMINE C₈ H₁₂ N BHHGXPLMPWCGHP-UHFFFAOYSA-O		Interactions Focus chain D [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYQ Query on TYQ	A	L-PEPTIDE LINKING	C₉ H₁₂ N₂ O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.161 (Depositor), 0.161 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.152 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.225 (Depositor)
R-Value Work: 0.198 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.22	α = 90
b = 62.144	β = 112.22
c = 92.344	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2023-09-20
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.