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- PDB-3x3y: Copper amine oxidase from Arthrobacter globiformis anaerobically ... -

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Basic information

Entry
Database: PDB / ID: 3x3y
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by histamine
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / Copper amine oxidase / 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, 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 ...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 / : / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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_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_alt_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)139,09219
Polymers137,8282
Non-polymers1,26417
Water22,1401229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-61 kcal/mol
Surface area40220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.471, 63.247, 157.906
Angle α, β, γ (deg.)90.000, 117.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1298-

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, 1246 molecules

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1229 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.35 %
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: BL44XU / Wavelength: 0.9
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. obs: 264870 / % possible obs: 98.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.74 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.425 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7


Resolution: 1.499→36.458 Å / SU ML: 0.11 / σ(F): 1.33 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 13274 5.03 %
Rwork0.1616 --
obs0.1623 263956 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.93 Å2
Refinement stepCycle: LAST / Resolution: 1.499→36.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 72 1229 11039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210375
X-RAY DIFFRACTIONf_angle_d1.07814165
X-RAY DIFFRACTIONf_dihedral_angle_d13.6793791
X-RAY DIFFRACTIONf_chiral_restr0.0721516
X-RAY DIFFRACTIONf_plane_restr0.0051895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4989-1.51590.25724060.22437611X-RAY DIFFRACTION90
1.5159-1.53370.23744240.20328325X-RAY DIFFRACTION97
1.5337-1.55240.22014520.19698210X-RAY DIFFRACTION97
1.5524-1.57210.21924770.198314X-RAY DIFFRACTION97
1.5721-1.59280.21474610.18148300X-RAY DIFFRACTION97
1.5928-1.61460.1964370.17738273X-RAY DIFFRACTION97
1.6146-1.63770.20893820.17428284X-RAY DIFFRACTION97
1.6377-1.66210.19534600.17318241X-RAY DIFFRACTION97
1.6621-1.68810.20724440.1728343X-RAY DIFFRACTION98
1.6881-1.71570.19014230.17348291X-RAY DIFFRACTION97
1.7157-1.74530.19944620.1728207X-RAY DIFFRACTION97
1.7453-1.77710.19734530.17138325X-RAY DIFFRACTION97
1.7771-1.81120.19194410.16678254X-RAY DIFFRACTION96
1.8112-1.84820.17854540.16618253X-RAY DIFFRACTION97
1.8482-1.88840.18363850.15838373X-RAY DIFFRACTION97
1.8884-1.93230.1884290.15628323X-RAY DIFFRACTION97
1.9323-1.98060.15894260.15788334X-RAY DIFFRACTION97
1.9806-2.03420.18114160.15698381X-RAY DIFFRACTION98
2.0342-2.0940.15844350.1558407X-RAY DIFFRACTION98
2.094-2.16160.17664590.15268503X-RAY DIFFRACTION99
2.1616-2.23890.16584570.15448463X-RAY DIFFRACTION99
2.2389-2.32850.16255130.15448464X-RAY DIFFRACTION99
2.3285-2.43450.17864230.15978584X-RAY DIFFRACTION100
2.4345-2.56280.18264640.16728507X-RAY DIFFRACTION100
2.5628-2.72330.16964510.16788590X-RAY DIFFRACTION100
2.7233-2.93350.18444080.16468610X-RAY DIFFRACTION100
2.9335-3.22850.16644500.15888638X-RAY DIFFRACTION100
3.2285-3.69530.1654700.14818583X-RAY DIFFRACTION100
3.6953-4.65420.15544440.13998459X-RAY DIFFRACTION97
4.6542-36.46880.17744680.17638232X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 30.014 Å / Origin y: 29.4998 Å / Origin z: 35.2637 Å
111213212223313233
T0.0356 Å2-0.0121 Å2-0.0046 Å2-0.0729 Å20.0162 Å2--0.0966 Å2
L0.318 °2-0.0284 °20.0671 °2-0.2129 °20.103 °2--1.2079 °2
S-0.0078 Å °0.0979 Å °0.0257 Å °-0.0179 Å °-0.0075 Å °-0.0145 Å °-0.0815 Å °0.1484 Å °0.0051 Å °
Refinement TLS groupSelection details: all

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