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- PDB-5zpe: Copper amine oxidase from Arthrobacter globiformis anaerobically ... -

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Basic information

Entry
Database: PDB / ID: 5zpe
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 288 K (2)
ComponentsPhenylethylamine oxidase
KeywordsSPLICING / COPPER AMINE OXIDASE / TOPAQUINONE / TPQ / OXIDOREDUCTASE
Function / homology
Function and homology information


primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
: / AGAO-like N2 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 ...: / AGAO-like N2 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: 1.689 Å
AuthorsMurakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Tanizawa, K. / Kumasaka, T. / Yamamoto, M. / Okajima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)0294 Japan
JSPS KAKENHI17K07317, JP26440037, JP23770127, JP15K05573, JP16KT0055 Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: In crystallothermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase
Authors: Murakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Kumasaka, T. / Yamamoto, M. / Tanizawa, K. / Okajima, T.
History
DepositionApr 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_conn.ptnr2_label_seq_id
Revision 1.4Nov 6, 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)138,0637
Polymers137,8282
Non-polymers2355
Water17,294960
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-72 kcal/mol
Surface area41530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.558, 64.465, 158.831
Angle α, β, γ (deg.)90.000, 117.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1313-

HOH

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Components

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / Source method: isolated from a natural source / Formula: H2O
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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 7.4 / Details: 1.05M potassium-sodium tartrate, 25mM HEPES

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 187451 / % possible obs: 97.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.29 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.053 / Rrim(I) all: 0.11 / Χ2: 3.832 / Net I/σ(I): 8.9 / Num. measured all: 780650
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.10.64690810.8070.3610.7410.94995.4
1.73-1.764.20.57692400.8490.320.660.97795.7
1.76-1.794.20.46891340.8960.260.5371.02395.9
1.79-1.834.20.40192010.9190.2220.4591.07996
1.83-1.874.20.33991990.9380.1880.3881.10796.1
1.87-1.914.20.27892860.9580.1540.3191.21496.3
1.91-1.964.20.23693190.9710.1310.271.32396.5
1.96-2.024.20.19792570.9770.1090.2261.43896.7
2.02-2.074.20.17792680.9780.0980.2031.57596.8
2.07-2.144.20.16593340.9760.0910.1891.74796.9
2.14-2.224.20.14693770.980.0810.1681.95597.3
2.22-2.314.20.13393420.9860.0740.1531.97697.3
2.31-2.414.20.12394300.9880.0680.1412.17897.6
2.41-2.544.20.11694100.9880.0640.1332.47497.8
2.54-2.74.20.10694930.9890.0590.1212.73697.9
2.7-2.914.20.09494600.990.0520.1073.65598.3
2.91-3.24.20.08495610.9910.0460.0965.26398.4
3.2-3.664.10.07695690.9890.0420.0868.27398.8
3.66-4.614.10.0796570.9930.0380.0814.06398.8
4.61-5040.06498330.9890.0350.07321.39998.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iu7

1iu7


Resolution: 1.689→40.411 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1727 9442 5.05 %
Rwork0.1512 177676 -
obs0.1523 187118 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.81 Å2 / Biso mean: 25.4891 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: final / Resolution: 1.689→40.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 8 960 10704
Biso mean--25.77 38.3 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610100
X-RAY DIFFRACTIONf_angle_d0.86513782
X-RAY DIFFRACTIONf_chiral_restr0.0611485
X-RAY DIFFRACTIONf_plane_restr0.0061836
X-RAY DIFFRACTIONf_dihedral_angle_d15.0985971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6894-1.70850.29932050.28793721392661
1.7085-1.72870.29093380.25285877621596
1.7287-1.74970.2673060.23435826613295
1.7497-1.77190.23613250.22295856618196
1.7719-1.79520.24573120.21585920623296
1.7952-1.81980.23133290.20575842617196
1.8198-1.84580.23073000.20435957625796
1.8458-1.87330.22782850.18465885617096
1.8733-1.90260.21123080.18315943625196
1.9026-1.93380.20162930.17635938623196
1.9338-1.96710.19493500.17045921627196
1.9671-2.00290.18763130.15545938625196
2.0029-2.04140.19053320.15575970630297
2.0414-2.08310.173260.15465945627197
2.0831-2.12840.19183010.15455939624097
2.1284-2.17790.1813150.14985994630997
2.1779-2.23240.16743140.14946001631597
2.2324-2.29270.17943130.14616036634997
2.2927-2.36020.17452980.15066008630697
2.3602-2.43630.1883080.15486036634497
2.4363-2.52340.19393080.1636037634598
2.5234-2.62440.18973270.16566098642598
2.6244-2.74380.18323160.16426040635698
2.7438-2.88850.18033050.15926108641398
2.8885-3.06940.17023400.15746103644398
3.0694-3.30630.17683320.14516079641198
3.3063-3.63880.14033480.12756133648199
3.6388-4.16490.12593360.116133646999
4.1649-5.24550.1173660.10376163652998
5.2455-40.42250.16332930.14716229652296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9775-0.4686-1.10652.66280.03661.45840.0789-0.13560.00880.3111-0.15570.2144-0.1309-0.34270.00330.2316-0.03140.06880.3794-0.08230.1713-49.18095.2261-0.9114
21.8581-0.27080.10240.4640.14830.7030.0008-0.56790.07480.2426-0.03850.03630.02-0.05590.06660.2787-0.06890.02880.39240.00680.1925-32.9048-2.34894.366
30.9519-0.03510.06940.2693-0.03790.89890.0059-0.29270.0320.0838-0.0078-0.0151-0.151-0.03120.00470.17-0.025-0.00330.1786-0.03070.1338-27.46034.0103-12.7722
40.37040.11340.0330.2635-0.00771.03640.0297-0.1044-0.01820.0394-0.0240.0091-0.0132-0.1405-0.00570.1-0.00690.00170.1288-0.00110.1213-37.1068-3.5516-24.9303
51.1984-0.00840.32950.25990.02641.0717-0.0117-0.04360.07440.0019-0.01340.0037-0.1021-0.1130.02520.1093-0.0009-0.00010.0946-0.01230.1327-34.96961.2777-31.0815
60.86580.2798-0.6343.4580.14462.67510.040.0138-0.0023-0.0463-0.0533-0.1498-0.02660.29550.02420.113-0.02980.03540.13640.04130.1414-11.39437.4566-69.4979
70.3895-0.0219-0.0320.2158-0.03080.95140.01110.01680.004-0.0291-0.00260.0018-0.06930.0037-0.00330.1144-0.0013-0.00030.0625-0.00570.1339-26.615-0.0415-51.1995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 72 )A9 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 124 )A73 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 277 )A125 - 277
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 581 )A278 - 581
5X-RAY DIFFRACTION5chain 'A' and (resid 582 through 628 )A582 - 628
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 72 )B9 - 72
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 628 )B73 - 628

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