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

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Basic information

Entry
Database: PDB / ID: 5zph
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH6 at 293K (2)
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
COPPER (II) ION / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMurakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Tanizawa, K. / Kumasaka, T. / Yamamoto, M. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
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 / 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 1.4Nov 20, 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
Water16,502916
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-74 kcal/mol
Surface area41640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.464, 64.505, 158.895
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1369-

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-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.: 916 / 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: 61.6 % / Mosaicity: 0.208 °
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: 293 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: 1.73→50 Å / Num. obs: 181520 / % possible obs: 98.9 % / Redundancy: 4 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.046 / Rrim(I) all: 0.094 / Χ2: 1.527 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.7640.70888110.7810.3980.8130.91898
1.76-1.794.10.59288860.8360.3330.680.94697.4
1.79-1.834.10.51388880.870.290.5910.99198.4
1.83-1.864.10.43789150.8950.2460.5031.01698.4
1.86-1.94.10.36388800.9240.2040.4171.06397.9
1.9-1.954.10.30589060.9450.1710.351.12698.2
1.95-240.24989790.9620.140.2861.299
2-2.0540.21589410.9710.1210.2471.23898.8
2.05-2.114.10.19589850.9750.110.2241.27498.7
2.11-2.184.10.17789740.9770.10.2031.38398.8
2.18-2.2640.15489910.9830.0870.1771.41299
2.26-2.354.10.13890260.9860.0780.1591.5299.1
2.35-2.4540.12990520.9880.0730.1481.56799.3
2.45-2.5840.12190500.9890.0680.1391.70199
2.58-2.7540.10690690.9920.060.1221.96399.7
2.75-2.9640.09390890.9930.0530.1072.28799.5
2.96-3.2640.07291460.9950.0410.0832.38299.8
3.26-3.733.90.05191510.9980.0290.0592.35699.8
3.73-4.693.90.03992150.9980.0220.0452.19799.8
4.69-503.80.03393710.9990.0190.0382.02999.4

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Processing

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

1iu7


Resolution: 1.72→40.437 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 9127 5.03 %
Rwork0.1533 172393 -
obs0.1545 180325 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.16 Å2 / Biso mean: 27.0818 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.72→40.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 4 916 10656
Biso mean--16.13 39.39 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610090
X-RAY DIFFRACTIONf_angle_d0.88413767
X-RAY DIFFRACTIONf_chiral_restr0.0611481
X-RAY DIFFRACTIONf_plane_restr0.0051834
X-RAY DIFFRACTIONf_dihedral_angle_d16.75958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7197-1.73920.28071890.2694409970
1.7392-1.75970.29492810.2441577298
1.7597-1.78110.25593150.2358566697
1.7811-1.80370.26052880.2242574998
1.8037-1.82740.24843110.2288571698
1.8274-1.85250.26662860.218570698
1.8525-1.87890.23753100.2009574399
1.8789-1.9070.21643180.1865572898
1.907-1.93680.1933200.1772573499
1.9368-1.96850.19863120.172575098
1.9685-2.00250.19623040.1608576499
2.0025-2.03890.18283320.1585576499
2.0389-2.07810.18023040.1583575098
2.0781-2.12050.1863090.15845777100
2.1205-2.16660.18443140.156578298
2.1666-2.2170.19423260.1583579399
2.217-2.27240.19593150.1561578299
2.2724-2.33390.19272810.1537579499
2.3339-2.40250.18453250.1567580099
2.4025-2.48010.18023350.1596580999
2.4801-2.56870.19082900.16735842100
2.5687-2.67150.19942950.1606585299
2.6715-2.79310.19053150.1638583199
2.7931-2.94030.18372850.1564591599
2.9403-3.12450.18293130.15345829100
3.1245-3.36560.15763290.14125865100
3.3656-3.70410.15283050.11895899100
3.7041-4.23960.12593210.11555919100
4.2396-5.33950.12932830.11075994100
5.3395-100.18563160.1625596998
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)
11.51790.4967-1.21244.3190.08082.22850.14840.21860.0498-0.396-0.2325-0.3335-0.09240.51050.02630.22850.03930.08160.34290.08440.176649.12195.44980.7534
23.40340.80320.36570.73690.18050.91910.01810.6740.2245-0.2182-0.0888-0.0893-0.00930.13530.06710.30130.07280.04910.37340.02880.218439.0073-1.2263-3.2952
31.22610.10840.20920.34030.17741.18030.01570.32570.0007-0.0986-0.00190.0211-0.1213-0.0017-0.0140.16530.0274-0.00710.15460.04290.133826.30863.380311.4608
40.4124-0.11310.01110.2666-0.0021.12920.02910.0848-0.0229-0.0392-0.0217-0.0083-0.01070.1323-0.00980.12670.0067-0.00450.1315-00.161336.9304-3.423924.8416
52.62890.41921.10780.16220.14821.2199-0.0205-0.05470.13-0.0103-0.03340.0077-0.1160.02480.04780.11910.0074-0.01240.08810.01870.129634.42331.367730.7222
61.1879-0.1885-1.21694.6851-0.30022.92560.02470.02020.0113-0.0037-0.04660.2471-0.0672-0.4519-0.02040.10460.0320.02540.1652-0.04770.162111.34697.431969.566
72.31870.0583-0.28260.14580.07190.9463-0.0286-0.3341-0.02780.10.0190.01260.0010.1759-0.0150.1718-0.01-0.02670.16990.00530.170636.0984-2.267473.0225
80.39240.0513-0.00110.26550.02821.070.01320.00380.00970.01710.0001-0.0044-0.0857-0.0497-0.00850.11440.0059-0.00760.06820.00420.151624.1560.528745.4403
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 114 )A73 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 277 )A115 - 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 191 )B73 - 191
8X-RAY DIFFRACTION8chain 'B' and (resid 192 through 628 )B192 - 628

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