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- PDB-7wno: Crystallographic structure of copper amine oxidase from Arthrobac... -

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Basic information

Entry
Database: PDB / ID: 7wno
TitleCrystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by only neutron diffraction data.
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / topaquinone / TPQ
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain
Similarity search - Domain/homology
COPPER (II) ION / DEUTERATED WATER / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodNEUTRON DIFFRACTION / MIR / Resolution: 1.72 Å
AuthorsMurakawa, T. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26440037 Japan
CitationJournal: Iucrj / Year: 2022
Title: Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.
Authors: Murakawa, T. / Kurihara, K. / Adachi, M. / Kusaka, K. / Tanizawa, K. / Okajima, T.
History
DepositionJan 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0572
Polymers68,9941
Non-polymers641
Water20,0691114
1
X: Phenylethylamine oxidase
hetero molecules

X: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,1154
Polymers137,9882
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15390 Å2
ΔGint-101 kcal/mol
Surface area39840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.548, 61.779, 92.232
Angle α, β, γ (deg.)90.00, 112.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1103-

DOD

21X-1220-

DOD

31X-1339-

DOD

41X-1589-

DOD

51X-1670-

DOD

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Components

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 68993.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46881, primary-amine oxidase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 1114 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 289 K / Method: microdialysis
Details: 1.05-M potassium sodium (Na) tartrate in 25-mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 3.0-5.7
DetectorType: iBIX / Detector: DIFFRACTOMETER / Date: Nov 10, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
131
25.71
ReflectionResolution: 1.72→20.94 Å / Num. obs: 76306 / % possible obs: 87.4 % / Redundancy: 2.664 % / Net I/σ(I): 4.99
Reflection shellResolution: 1.72→1.78 Å

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.72→20.94 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 3814 5 %
Rwork0.163 --
obs0.168 76241 87.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.00613232
NEUTRON DIFFRACTIONf_angle_d1.14121005
NEUTRON DIFFRACTIONf_dihedral_angle_d17.4943123
NEUTRON DIFFRACTIONf_chiral_restr0.065764
NEUTRON DIFFRACTIONf_plane_restr0.0082305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.3386990.26391877NEUTRON DIFFRACTION62
1.74-1.760.35651090.28352057NEUTRON DIFFRACTION67
1.76-1.790.39611150.27062207NEUTRON DIFFRACTION73
1.79-1.810.38551210.26142291NEUTRON DIFFRACTION75
1.81-1.840.34021260.24812400NEUTRON DIFFRACTION78
1.84-1.870.33611260.23362396NEUTRON DIFFRACTION78
1.87-1.90.2961280.21542417NEUTRON DIFFRACTION80
1.9-1.930.30861320.20772514NEUTRON DIFFRACTION81
1.93-1.970.29471360.20852597NEUTRON DIFFRACTION85
1.97-2.010.31271370.20512589NEUTRON DIFFRACTION86
2.01-2.050.31981430.19332733NEUTRON DIFFRACTION89
2.05-2.090.30141460.1882766NEUTRON DIFFRACTION90
2.09-2.140.26681480.17972817NEUTRON DIFFRACTION92
2.14-2.190.32331510.17292867NEUTRON DIFFRACTION94
2.19-2.250.28611470.1622769NEUTRON DIFFRACTION91
2.25-2.320.25941470.14572805NEUTRON DIFFRACTION92
2.32-2.390.24341540.13792919NEUTRON DIFFRACTION95
2.39-2.480.21531560.14542977NEUTRON DIFFRACTION96
2.48-2.580.25231540.15152944NEUTRON DIFFRACTION96
2.58-2.70.30291580.15382991NEUTRON DIFFRACTION97
2.7-2.840.241590.1573019NEUTRON DIFFRACTION98
2.84-3.020.23811590.15153016NEUTRON DIFFRACTION98
3.02-3.250.22051600.13983047NEUTRON DIFFRACTION98
3.25-3.570.21241560.1222955NEUTRON DIFFRACTION96
3.57-4.090.18991550.11292961NEUTRON DIFFRACTION96
4.09-5.130.18181530.11212879NEUTRON DIFFRACTION92
5.14-20.940.20921390.14082617NEUTRON DIFFRACTION82

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