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- PDB-3wa2: High resolution crystal structure of copper amine oxidase from ar... -

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Basic information

Entry
Database: PDB / ID: 3wa2
TitleHigh resolution crystal structure of copper amine oxidase from arthrobacter globiformis
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / oxidase / copper binding / post-translationally derived quinone cofactor
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
COPPER (II) ION / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsMurakawa, T. / Hayashi, H. / Sunami, T. / Kurihara, K. / Tamada, T. / Kuroki, R. / Suzuki, M. / Tanizawa, K. / Okajima, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2
Authors: Murakawa, T. / Hayashi, H. / Sunami, T. / Kurihara, K. / Tamada, T. / Kuroki, R. / Suzuki, M. / Tanizawa, K. / Okajima, T.
History
DepositionApr 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 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_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.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_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_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_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
X: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,34636
Polymers69,0101
Non-polymers3,33635
Water16,304905
1
X: Phenylethylamine oxidase
hetero molecules

X: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,69272
Polymers138,0202
Non-polymers6,67270
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13750 Å2
ΔGint-44 kcal/mol
Surface area40810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.745, 62.379, 92.076
Angle α, β, γ (deg.)90.00, 112.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1581-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 69009.836 Da / Num. of mol.: 1 / Fragment: UNP residues 9-629
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

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Non-polymers , 9 types, 940 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 289 K / pH: 6.8
Details: 1.05 M potassium tartrate, 25 mM HEPES (pH 6.8), MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 19, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.08→100 Å / Num. obs: 663537 / % possible obs: 95.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 9.92 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.08-1.12.40.4441,263.3
1.1-1.122.70.3871,276.2
1.12-1.143.10.3521,287.6
1.14-1.163.20.311,292.6
1.16-1.193.30.2951,296.5
1.19-1.223.40.2721,298.9
1.22-1.253.50.2511,299.9
1.25-1.283.70.2291,2100
1.28-1.323.70.1941,2100
1.32-1.363.70.1661,2100
1.36-1.413.70.1381,2100
1.41-1.473.80.1111,2100
1.47-1.533.80.0881,2100
1.53-1.613.80.0731,2100
1.61-1.713.80.0681,2100
1.71-1.853.80.0731,299.9
1.85-2.034.40.0831,299.9
2.03-2.337.70.071,2100
2.33-2.937.70.0471,2100
2.93-1005.90.0521,293.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iu7

1iu7


Resolution: 1.08→31.97 Å / Occupancy max: 1 / Occupancy min: 0.08 / SU ML: 0.09 / Phase error: 14.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.15 15331 5.02 %
Rwork0.13 --
obs0.131 305197 86.5 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.06 Å2
Refinement stepCycle: LAST / Resolution: 1.08→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 216 905 5997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115739
X-RAY DIFFRACTIONf_angle_d1.5827828
X-RAY DIFFRACTIONf_dihedral_angle_d15.9832262
X-RAY DIFFRACTIONf_chiral_restr0.088840
X-RAY DIFFRACTIONf_plane_restr0.0091038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0808-1.0930.25983180.2455467X-RAY DIFFRACTION49
1.093-1.10590.25573300.23536487X-RAY DIFFRACTION59
1.1059-1.11940.24094090.22457384X-RAY DIFFRACTION66
1.1194-1.13360.2234720.21648173X-RAY DIFFRACTION73
1.1336-1.14850.234380.20328534X-RAY DIFFRACTION77
1.1485-1.16420.22124710.19178868X-RAY DIFFRACTION80
1.1642-1.18090.19864840.18289110X-RAY DIFFRACTION82
1.1809-1.19850.19565010.17129246X-RAY DIFFRACTION83
1.1985-1.21720.19544670.15529429X-RAY DIFFRACTION85
1.2172-1.23720.17024920.14839464X-RAY DIFFRACTION85
1.2372-1.25850.16135300.14049590X-RAY DIFFRACTION86
1.2585-1.28140.16685050.1369749X-RAY DIFFRACTION87
1.2814-1.3060.15135230.12989782X-RAY DIFFRACTION88
1.306-1.33270.14965330.12259794X-RAY DIFFRACTION88
1.3327-1.36170.14425100.116810025X-RAY DIFFRACTION90
1.3617-1.39330.13955560.113710029X-RAY DIFFRACTION90
1.3933-1.42820.13625360.105910066X-RAY DIFFRACTION90
1.4282-1.46680.13415380.105810197X-RAY DIFFRACTION91
1.4668-1.510.13275450.101610274X-RAY DIFFRACTION92
1.51-1.55870.12985110.099210389X-RAY DIFFRACTION93
1.5587-1.61440.125770.098110387X-RAY DIFFRACTION94
1.6144-1.6790.1245420.101710550X-RAY DIFFRACTION94
1.679-1.75540.13465470.10810458X-RAY DIFFRACTION94
1.7554-1.8480.13155750.110610614X-RAY DIFFRACTION95
1.848-1.96380.12675490.115710717X-RAY DIFFRACTION96
1.9638-2.11540.12565720.112611004X-RAY DIFFRACTION98
2.1154-2.32820.13335890.114611107X-RAY DIFFRACTION99
2.3282-2.66490.1375820.128811196X-RAY DIFFRACTION99
2.6649-3.35690.16256130.139511244X-RAY DIFFRACTION100
3.3569-31.98640.16525160.14710532X-RAY DIFFRACTION92

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