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- PDB-3x41: Copper amine oxidase from Arthrobacter globiformis: Product Schif... -

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Basic information

Entry
Database: PDB / ID: 3x41
TitleCopper amine oxidase from Arthrobacter globiformis: Product Schiff-base form produced by anaerobic reduction in the presence of sodium bromide
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / Copper amine oxidase / topaquinone / TPQ
Function / homology
Function and homology information


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
BROMIDE ION / COPPER (II) ION / : / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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_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.pdbx_dist_value / _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
Revision 1.3Nov 13, 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)140,48833
Polymers138,0322
Non-polymers2,45631
Water20,3211128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-82 kcal/mol
Surface area39030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.619, 63.290, 157.851
Angle α, β, γ (deg.)90.000, 117.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1259-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 69015.883 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 , 6 types, 1159 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1128 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
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: 0.919
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.7→47.246 Å / Num. obs: 137175 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 12.9
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.399 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7


Resolution: 1.87→31.881 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 6880 5.02 %
Rwork0.1515 --
obs0.1529 137073 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.06 Å2
Refinement stepCycle: LAST / Resolution: 1.87→31.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9754 0 116 1128 10998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410183
X-RAY DIFFRACTIONf_angle_d1.11213857
X-RAY DIFFRACTIONf_dihedral_angle_d13.9813706
X-RAY DIFFRACTIONf_chiral_restr0.0761475
X-RAY DIFFRACTIONf_plane_restr0.0051836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89120.23692300.2054203X-RAY DIFFRACTION97
1.8912-1.91350.24922310.19864272X-RAY DIFFRACTION97
1.9135-1.93680.22972200.19374221X-RAY DIFFRACTION97
1.9368-1.96130.23272050.18044280X-RAY DIFFRACTION97
1.9613-1.98710.22082330.18364267X-RAY DIFFRACTION97
1.9871-2.01440.2142280.17784288X-RAY DIFFRACTION98
2.0144-2.04310.24412150.16884307X-RAY DIFFRACTION98
2.0431-2.07360.20492240.16284264X-RAY DIFFRACTION98
2.0736-2.1060.18072400.15844353X-RAY DIFFRACTION98
2.106-2.14050.19472260.15614253X-RAY DIFFRACTION98
2.1405-2.17740.18662570.15414327X-RAY DIFFRACTION98
2.1774-2.2170.17882270.15324250X-RAY DIFFRACTION98
2.217-2.25970.1872280.15144356X-RAY DIFFRACTION98
2.2597-2.30580.16852270.14784316X-RAY DIFFRACTION99
2.3058-2.35590.18292250.14664368X-RAY DIFFRACTION99
2.3559-2.41070.20162280.14774356X-RAY DIFFRACTION99
2.4107-2.47090.17992410.14944321X-RAY DIFFRACTION99
2.4709-2.53770.17232310.14534357X-RAY DIFFRACTION99
2.5377-2.61240.18472420.14584314X-RAY DIFFRACTION99
2.6124-2.69660.18122180.15244380X-RAY DIFFRACTION99
2.6966-2.7930.17752280.15244374X-RAY DIFFRACTION99
2.793-2.90470.19172270.14434381X-RAY DIFFRACTION99
2.9047-3.03680.15352140.14134399X-RAY DIFFRACTION99
3.0368-3.19680.15462270.13924377X-RAY DIFFRACTION99
3.1968-3.39690.15942400.13744385X-RAY DIFFRACTION99
3.3969-3.65880.15812180.13314422X-RAY DIFFRACTION99
3.6588-4.02640.15532400.13244417X-RAY DIFFRACTION99
4.0264-4.60750.14382300.13214449X-RAY DIFFRACTION100
4.6075-5.79920.18512310.14824459X-RAY DIFFRACTION99
5.7992-31.88540.20652490.19434477X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 29.8549 Å / Origin y: 0.6086 Å / Origin z: 35.2611 Å
111213212223313233
T0.087 Å20.0059 Å2-0.0106 Å2-0.0784 Å20.0092 Å2--0.1526 Å2
L0.3044 °2-0.0115 °2-0.1766 °2-0.2137 °20.0773 °2--1.4608 °2
S0.0146 Å °0.0477 Å °0.0355 Å °-0.0195 Å °-0.0157 Å °-0.0122 Å °-0.1377 Å °0.0191 Å °0.0024 Å °
Refinement TLS groupSelection details: ALL

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