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

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Basic information

Entry
Database: PDB / ID: 5zpr
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 9 at 288 K (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, 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 / PHENYLACETALDEHYDE / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 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 / struct_conn_type
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_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_asym_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.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 / _struct_conn_type.id
Revision 1.4Nov 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)138,38811
Polymers137,8282
Non-polymers5609
Water18,7361040
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,28710
Polymers137,8282
Non-polymers4598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14230 Å2
ΔGint-104 kcal/mol
Surface area40660 Å2
MethodPISA
2
B: Phenylethylamine oxidase
hetero molecules

B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,48912
Polymers137,8282
Non-polymers66210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14800 Å2
ΔGint-53 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.849, 64.320, 159.026
Angle α, β, γ (deg.)90.000, 116.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1093-

HOH

21A-1162-

HOH

31A-1277-

HOH

41B-1137-

HOH

51B-1231-

HOH

61B-1293-

HOH

71B-1327-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 1049 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 3.19 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: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 129153 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.22 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.062 / Rrim(I) all: 0.117 / Χ2: 1.557 / Net I/σ(I): 7.2 / Num. measured all: 444214
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.953.10.66163200.6960.450.8031.07995.9
1.95-1.993.10.54963130.7640.3720.6661.10296.2
1.99-2.033.10.47963300.8190.3230.5811.18896.2
2.03-2.073.10.41463470.8560.2760.51.20696.3
2.07-2.113.20.37663110.8690.2480.4531.24696.3
2.11-2.163.20.33863720.8870.2190.4041.31596.4
2.16-2.223.30.29663390.9180.1920.3541.37796.5
2.22-2.283.30.26463570.9290.1690.3141.4596.9
2.28-2.343.40.23764430.940.1510.2811.48697.3
2.34-2.423.40.21664460.9530.1360.2561.52797.6
2.42-2.513.50.19964190.9590.1240.2351.54497.8
2.51-2.613.60.17764980.9670.1090.2091.58198
2.61-2.723.70.15465170.9750.0930.181.70898.3
2.72-2.873.70.12964680.9820.0780.1521.72798.3
2.87-3.053.70.10865430.9860.0650.1271.92698.4
3.05-3.283.70.08665260.9910.0520.1012.05198.6
3.28-3.613.70.06565740.9940.040.0772.07398.6
3.61-4.143.70.0565830.9960.0310.0591.87398.9
4.14-5.213.60.03866390.9980.0230.0451.64298.8
5.21-503.50.03368080.9980.0210.0391.4499

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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: 1.922→40.429 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 18.96
RfactorNum. reflection% reflection
Rfree0.182 6393 4.96 %
Rwork0.1483 --
obs0.1499 128991 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.44 Å2 / Biso mean: 21.8756 Å2 / Biso min: 4.47 Å2
Refinement stepCycle: final / Resolution: 1.922→40.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 31 1040 10809
Biso mean--22.47 36.22 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710130
X-RAY DIFFRACTIONf_angle_d0.8713822
X-RAY DIFFRACTIONf_chiral_restr0.061494
X-RAY DIFFRACTIONf_plane_restr0.0061844
X-RAY DIFFRACTIONf_dihedral_angle_d15.6826008
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 (%)
1.9216-1.94340.28671920.2553819401191
1.9434-1.96630.2692200.2393964418496
1.9663-1.99030.26732080.22124024423296
1.9903-2.01550.26482040.21654021422596
2.0155-2.0420.24321910.20694029422096
2.042-2.070.24442010.19684050425196
2.07-2.09950.24142010.19564003420496
2.0995-2.13090.19722200.18034030425096
2.1309-2.16420.21651950.17224068426396
2.1642-2.19960.20072140.1724032424697
2.1996-2.23760.23841950.16554011420696
2.2376-2.27820.19562130.16284050426397
2.2782-2.32210.20852300.15564040427097
2.3221-2.36950.22352070.15274135434297
2.3695-2.4210.19412110.1514076428798
2.421-2.47730.18522190.15084124434398
2.4773-2.53920.18552200.14934058427898
2.5392-2.60790.20172230.15084102432598
2.6079-2.68460.18062120.15224136434898
2.6846-2.77120.20362080.1544111431998
2.7712-2.87020.18592130.154110432398
2.8702-2.98510.19412290.14624130435998
2.9851-3.12090.16352120.14374158437098
3.1209-3.28540.18242160.14074162437899
3.2854-3.49110.16072070.12574166437399
3.4911-3.76050.13272440.11434157440199
3.7605-4.13860.13382220.10374168439099
4.1386-4.73670.11712040.09644190439499
4.7367-5.96470.14312110.12114277448899
5.9647-40.43760.16962510.1554197444896
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)
10.6797-0.0229-0.16350.6812-0.0560.04770.0872-0.1110.02940.2435-0.16930.114-0.2567-0.2146-0.2460.17650.08890.04940.1819-0.08930.093-17.970422.637534.7276
20.4508-0.126-0.13230.27010.13460.631-0.0153-0.3202-0.0270.1768-0.01120.0195-0.00730.1447-0.03620.1309-0.0252-0.01460.18820.01170.11776.748113.155537.4698
30.27710.08420.0640.1928-0.02091.08320.0101-0.02170.00920.0217-0.00810.0019-0.1129-0.08820.04270.05040.01150.00340.0402-0.00290.0755-6.044216.371910.0667
40.2074-0.29830.04970.6406-0.07040.02910.06110.0090.0104-0.1806-0.07440.0094-0.06490.18370.0050.1619-0.0270.04950.1540.03040.1182-17.907-5.842935.0381
50.20860.0024-0.00230.455-0.0130.3369-0.07090.038-0.1513-0.2525-0.0608-0.3246-0.00420.2855-0.20530.13930.00010.04590.14930.01210.1603-14.6541-14.595236.5989
60.1061-0.0264-0.04620.0756-0.05740.05630.04350.30390.0225-0.1449-0.0368-0.02-0.0035-0.13020.00110.15370.0279-0.01630.2465-0.00730.1516-47.6281-16.338631.3304
70.72670.0305-0.16650.2598-0.11160.77630.01670.19920.0281-0.1156-0.0004-0.0036-0.22360.01340.11460.0680.031-0.01570.00250.00750.0498-36.9462-10.704749.7237
80.2159-0.0501-0.01810.1994-0.02460.8460.02420.0188-0.0172-0.0175-0.01220.0043-0.0470.05080.00470.060.00020.00260.0392-0.00420.0843-30.1594-16.104762.8167
90.0928-0.01960.06550.034-0.10840.62520.00450.0175-0.0234-0.0471-0.013-0.0130.03520.1036-0.00010.06480.0091-0.00190.0638-0.00830.1-27.3519-22.212658.2589
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 44 )B9 - 44
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 95 )B45 - 95
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 138 )B96 - 138
7X-RAY DIFFRACTION7chain 'B' and (resid 139 through 277 )B139 - 277
8X-RAY DIFFRACTION8chain 'B' and (resid 278 through 516 )B278 - 516
9X-RAY DIFFRACTION9chain 'B' and (resid 517 through 628 )B517 - 628

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