Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.08 kDa 
• Atom Count: 5858 
• Modelled Residue Count: 620 
• Deposited Residue Count: 621 
• Unique protein chains: 1

7WNP

Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution.

• PDB DOI: 10.2210/pdb7WNP/pdb

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


• Deposited: 2022-01-19 Released: 2022-04-20 
• Deposition Author(s): Murakawa, T., Okajima, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.189 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

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• Method: NEUTRON DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.235 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.

Murakawa, T., Kurihara, K., Adachi, M., Kusaka, K., Tanizawa, K., Okajima, T.

(2022) IUCrJ 9: 342-348

• PubMed: 35546796 
• DOI: 10.1107/S2052252522003657
• Primary Citation of Related Structures:  
  7WNO, 7WNP


• PubMed Abstract: 
  

Protein neutron crystallography is a powerful technique to determine the positions of H atoms, providing crucial biochemical information such as the protonation states of catalytic groups and the geometry of hydrogen bonds. Recently, the crystal structure of a bacterial copper amine oxidase was determined by joint refinement using X-ray and neutron diffraction data sets at resolutions of 1.14 and 1.72 Å, respectively [Murakawa et al. (2020 ▸). Proc. Natl Acad. Sci. USA , 117 , 10818-10824]. While joint refinement is effective for the determination of the accurate positions of heavy atoms on the basis of the electron density, the structural information on light atoms (hydrogen and deuterium) derived from the neutron diffraction data might be affected by the X-ray data. To unravel the information included in the neutron diffraction data, the structure determination was conducted again using only the neutron diffraction data at 1.72 Å resolution and the results were compared with those obtained in the previous study. Most H and D atoms were identified at essentially the same positions in both the neutron-only and the X-ray/neutron joint refinements. Nevertheless, neutron-only refinement was found to be less effective than joint refinement in providing very accurate heavy-atom coordinates that lead to significant improvement of the neutron scattering length density map, especially for the active-site cofactor. Consequently, it was confirmed that X-ray/neutron joint refinement is crucial for determination of the real chemical structure of the catalytic site of the enzyme.

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Organizational Affiliation: 

Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethylamine oxidase	A [auth X]	621	Arthrobacter globiformis	Mutation(s): 0  EC: 1.4.3.21
UniProt
Find proteins for P46881 (Arthrobacter globiformis) Explore P46881  Go to UniProtKB:  P46881

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth X]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	C [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ASA	A [auth X]	L-PEPTIDE LINKING	C4 H7 N O3		ASP
TPQ	A [auth X]	L-PEPTIDE LINKING	C9 H9 N O5		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.189 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: C 1 2 1

• Method: NEUTRON DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.235 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.206	α = 90
b = 61.979	β = 112.06
c = 92.447	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2022-01-19 
• Released Date: 2022-04-20 
Deposition Author(s): Murakawa, T., Okajima, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP26440037

Revision History  

• Version 1.0: 2022-04-20
  Type: Initial release
  
• Version 1.1: 2022-05-25
  Changes: Database references