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- PDB-3x3x: Copper amine oxidase from Arthrobacter globiformis anaerobically ... -

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Basic information

Entry
Database: PDB / ID: 3x3x
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / Copper amine oxidase / topaquinone / TPQ
Function / homology
Function and homology information


aliphatic amine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
: / AGAO-like N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / : / Copper amine oxidase copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase ...: / AGAO-like N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / : / Copper amine oxidase copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / 2-PHENYL-ETHANOL / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsOkajima, T. / Nakanishi, S. / Murakawa, T. / Kataoka, M. / Hayashi, H. / Hamaguchi, A. / Nakai, T. / Kawano, Y. / Yamaguchi, H. / Tanizawa, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions.
Authors: Murakawa, T. / Hamaguchi, A. / Nakanishi, S. / Kataoka, M. / Nakai, T. / Kawano, Y. / Yamaguchi, H. / Hayashi, H. / Tanizawa, K. / Okajima, T.
History
DepositionMar 10, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylethylamine oxidase
B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,91316
Polymers137,8282
Non-polymers1,08514
Water20,9691164
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,39622
Polymers137,8282
Non-polymers1,56920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area17710 Å2
ΔGint-76 kcal/mol
Surface area39200 Å2
MethodPISA
2
B: Phenylethylamine oxidase
hetero molecules

B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,42910
Polymers137,8282
Non-polymers6028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14280 Å2
ΔGint-69 kcal/mol
Surface area40080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.658, 62.890, 158.006
Angle α, β, γ (deg.)90.000, 117.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1355-

HOH

21B-1246-

HOH

31B-1348-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 68913.750 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 9-628
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: pEPO-2 / Production host: Escherichia coli (E. coli) / Strain (production host): CD03 / References: UniProt: P46881, primary-amine oxidase

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Non-polymers , 5 types, 1178 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEL / 2-PHENYL-ETHANOL


Mass: 122.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1164 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 289 K / pH: 6.8
Details: 1.05M potassium-sodium tartrate, 25mM HEPES (pH6.8), MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.57→38.519 Å / Num. obs: 228324 / % possible obs: 98.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.85 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 16.7
Reflection shellResolution: 1.57→1.65 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.392 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7


Resolution: 1.57→20.414 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 11432 5.01 %
Rwork0.2149 --
obs0.2163 228275 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.8092 Å2
Refinement stepCycle: LAST / Resolution: 1.57→20.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 65 1164 10967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110060
X-RAY DIFFRACTIONf_angle_d1.05313657
X-RAY DIFFRACTIONf_dihedral_angle_d13.3213650
X-RAY DIFFRACTIONf_chiral_restr0.0441466
X-RAY DIFFRACTIONf_plane_restr0.0051816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.58780.30523600.26186945X-RAY DIFFRACTION95
1.5878-1.60650.30463730.25767067X-RAY DIFFRACTION96
1.6065-1.62610.30663730.25517085X-RAY DIFFRACTION96
1.6261-1.64670.30093660.24837015X-RAY DIFFRACTION96
1.6467-1.66830.28933610.23467086X-RAY DIFFRACTION97
1.6683-1.69120.25873950.22947117X-RAY DIFFRACTION97
1.6912-1.71530.26983520.23367128X-RAY DIFFRACTION97
1.7153-1.74090.26763890.23587184X-RAY DIFFRACTION98
1.7409-1.76810.29353500.23467202X-RAY DIFFRACTION98
1.7681-1.79710.25694090.22977206X-RAY DIFFRACTION98
1.7971-1.8280.26363460.2337156X-RAY DIFFRACTION98
1.828-1.86130.26063800.2347265X-RAY DIFFRACTION98
1.8613-1.8970.27863890.22437218X-RAY DIFFRACTION98
1.897-1.93570.25313810.22917233X-RAY DIFFRACTION99
1.9357-1.97780.26464110.22177293X-RAY DIFFRACTION99
1.9778-2.02370.24253610.21917280X-RAY DIFFRACTION99
2.0237-2.07430.26663730.237241X-RAY DIFFRACTION99
2.0743-2.13030.25714060.22367264X-RAY DIFFRACTION99
2.1303-2.19290.24554040.21767303X-RAY DIFFRACTION99
2.1929-2.26360.2463870.22037307X-RAY DIFFRACTION100
2.2636-2.34440.26183880.22537381X-RAY DIFFRACTION100
2.3444-2.43820.26043600.22077371X-RAY DIFFRACTION100
2.4382-2.54890.24093840.22237383X-RAY DIFFRACTION100
2.5489-2.6830.24363490.22327396X-RAY DIFFRACTION100
2.683-2.85070.24653980.22087290X-RAY DIFFRACTION99
2.8507-3.07010.23873900.21067179X-RAY DIFFRACTION97
3.0701-3.37790.22193850.2027171X-RAY DIFFRACTION97
3.3779-3.86380.2233820.19077280X-RAY DIFFRACTION98
3.8638-4.85710.19164100.18077379X-RAY DIFFRACTION99
4.8571-20.41530.2114200.19727418X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 18.8263 Å / Origin y: -47.6831 Å / Origin z: -34.9241 Å
111213212223313233
T0.0702 Å20.0186 Å2-0.0022 Å2-0.0627 Å2-0.0069 Å2--0.0827 Å2
L0.0652 °20.1173 °2-0.1977 °2-0.048 °2-0.1631 °2--0.3464 °2
S0.0142 Å °0.0017 Å °-0.0123 Å °0.0164 Å °-0.0184 Å °-0.0032 Å °-0.04 Å °0.0096 Å °-0.0145 Å °
Refinement TLS groupSelection details: ALL

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