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- PDB-5zp9: Copper amine oxidase from Arthrobacter globiformis anaerobically ... -

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Basic information

Entry
Database: PDB / ID: 5zp9
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 283 K (1)
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, 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: 1.7 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 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Nov 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)138,0016
Polymers137,8282
Non-polymers1734
Water18,0151000
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-73 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.531, 64.276, 158.846
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-1380-

HOH

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Components

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 68913.750 Da / Num. of mol.: 2
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-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1000 / 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: 3.19 Å3/Da / Density % sol: 61.44 %
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: 283 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: 190856 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.91 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.047 / Rrim(I) all: 0.095 / Χ2: 1.689 / Net I/σ(I): 8.1 / Num. measured all: 782126
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.10.68495490.7990.3890.7891.031100
1.73-1.764.10.61294030.840.3460.7041.052100
1.76-1.794.10.595410.8880.2830.5761.074100
1.79-1.834.10.42993950.9040.2430.4941.119100
1.83-1.874.10.35695260.9320.2010.4091.142100
1.87-1.914.10.29495050.950.1660.3391.195100
1.91-1.964.10.2495140.9690.1350.2761.254100
1.96-2.024.10.20395160.9760.1150.2341.297100
2.02-2.074.10.17895480.980.10.2041.361100
2.07-2.144.10.16294690.9830.0910.1861.406100
2.14-2.224.10.1495330.9850.0780.1611.489100
2.22-2.314.20.12895260.9880.0720.1471.593100
2.31-2.414.10.12294920.9880.0690.141.741100
2.41-2.544.10.12195650.9880.0680.142.036100
2.54-2.74.10.11595490.9890.0650.1322.43100
2.7-2.914.10.195860.990.0570.1152.779100
2.91-3.240.08295550.9930.0470.0953.051100
3.2-3.664.10.05795860.9960.0320.0662.667100
3.66-4.6140.04196800.9980.0230.0482.23699.9
4.61-503.90.03498180.9990.0190.0391.8999.7

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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: 1.7→39.66 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1704 9547 5.01 %
Rwork0.1514 --
obs0.1524 190659 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.22 Å2 / Biso mean: 24.6329 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.7→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 4 1000 10740
Biso mean--13.56 37.71 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610144
X-RAY DIFFRACTIONf_angle_d0.88213848
X-RAY DIFFRACTIONf_chiral_restr0.0611491
X-RAY DIFFRACTIONf_plane_restr0.0061847
X-RAY DIFFRACTIONf_dihedral_angle_d17.3826004
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 (%)
1.6997-1.7190.26952720.25185706597895
1.719-1.73930.26442950.247260266321100
1.7393-1.76050.27183150.236360406355100
1.7605-1.78280.26813280.247460106338100
1.7828-1.80620.27273420.225759606302100
1.8062-1.8310.25463510.220159516302100
1.831-1.85710.23933250.204360886413100
1.8571-1.88480.21363160.192360286344100
1.8848-1.91430.21933280.182459616289100
1.9143-1.94570.21143190.17560396358100
1.9457-1.97920.1943040.163559976301100
1.9792-2.01520.19433300.161360756405100
2.0152-2.0540.1752930.161659976290100
2.054-2.09590.18213370.160260306367100
2.0959-2.14150.1693200.154360426362100
2.1415-2.19130.14983150.147160326347100
2.1913-2.24610.17353080.146460596367100
2.2461-2.30680.1793280.147360406368100
2.3068-2.37470.15093230.143860676390100
2.3747-2.45130.183140.15460036317100
2.4513-2.53890.18093200.156660836403100
2.5389-2.64050.17333340.154660026336100
2.6405-2.76070.18023210.15860866407100
2.7607-2.90620.173330.153960676400100
2.9062-3.08820.18093290.15260486377100
3.0882-3.32650.17113310.143760616392100
3.3265-3.66110.13692970.122761046401100
3.6611-4.19040.11733250.112761266451100
4.1904-5.27740.11452890.105161646453100
5.2774-39.67060.1553050.15096220652598
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)
10.98420.4352-1.053.0997-0.04681.55020.08390.18240.032-0.3897-0.1651-0.2163-0.07330.3627-0.02750.22040.04030.0650.30180.0760.159549.05385.38230.7326
21.367-0.02280.12840.2786-0.08810.35640.01910.5518-0.068-0.1895-0.0324-0.01820.027-0.0350.01110.23160.0513-0.00430.3789-0.02570.170724.2743-3.9246-2.1566
30.366-0.0818-0.00170.2590.00880.89010.020.08870.0041-0.0353-0.0187-0.0047-0.06620.1095-0.00050.11380.0017-0.00240.11980.00440.134936.2728-0.232325.2848
40.8025-0.0599-0.89073.4776-0.10932.27920.00550.00190.01790.0243-0.02960.1777-0.0318-0.308-0.02570.10370.02240.02860.136-0.04150.137611.44367.391269.5378
50.36050.019-0.02730.19890.03340.8690.0061-0.0240.00230.0322-0.00230.0003-0.0604-0.0005-0.00080.1171-0.0008-0.00370.07130.00530.139526.6394-0.115851.1426
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 191 )A73 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 628 )A192 - 628
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 72 )B9 - 72
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 628 )B73 - 628

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