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

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Basic information

Entry
Database: PDB / ID: 5zpp
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 8 at 288 K (3)
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: 1.81 Å
AuthorsMurakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Tanizawa, K. / Kumasaka, T. / Yamamoto, M. / Okajima, T.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)0294 Japan
Japan Society for the Promotion of Science17K07317 Japan
Japan Society for the Promotion of ScienceJP26440037 Japan
Japan Society for the Promotion of ScienceJP23770127 Japan
Japan Society for the Promotion of ScienceJP15K05573 Japan
Japan Society for the Promotion of ScienceJP16KT0055 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 23, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
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 / 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 1.3Nov 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)138,51213
Polymers137,8282
Non-polymers68511
Water17,691982
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,53514
Polymers137,8282
Non-polymers70812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area16030 Å2
ΔGint-82 kcal/mol
Surface area40540 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_756-x+2,y,-z+11
Buried area15830 Å2
ΔGint-67 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.019, 64.746, 158.925
Angle α, β, γ (deg.)90.00, 117.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1116-

HOH

21A-1246-

HOH

31B-1052-

HOH

41B-1194-

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, 993 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 3.21 Å3/Da / Density % sol: 61.68 %
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 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 157934 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.45 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.062 / Rrim(I) all: 0.127 / Χ2: 2.949 / Net I/σ(I): 7.1 / Num. measured all: 657858
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.81-1.844.20.72577800.730.4030.831.05698.1
1.84-1.874.20.61477400.7730.3410.7041.07298
1.87-1.914.20.51178320.8420.2840.5851.12298.2
1.91-1.954.20.43578000.8740.2420.4991.21398.3
1.95-1.994.20.36178060.9020.2010.4141.21798.4
1.99-2.044.20.3278320.9220.1780.3671.33798.5
2.04-2.094.20.28878290.9330.1610.3311.30598.6
2.09-2.154.20.25578310.9440.1420.2931.35398.7
2.15-2.214.20.22778270.9510.1270.2611.44298.8
2.21-2.284.20.20378710.960.1130.2331.51798.9
2.28-2.364.20.18678740.9580.1040.2131.76999
2.36-2.464.20.1778710.9690.0950.1951.67199.1
2.46-2.574.20.15579100.9750.0870.1781.66299.2
2.57-2.74.20.14179580.9770.0790.1611.99699.4
2.7-2.874.20.12678960.9760.0710.1452.53299.4
2.87-3.094.20.10380010.9830.0580.1192.80599.6
3.09-3.414.10.08279870.9880.0450.0943.95699.7
3.41-3.94.10.06480070.990.0360.0735.32299.7
3.9-4.914.10.05280550.990.0290.068.39699.8
4.91-503.90.05382270.9840.0310.06216.88899.6

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Processing

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

1iu7


Resolution: 1.81→40.51 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.169 7991 5.07 %
Rwork0.144 --
obs0.145 157670 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.44 Å2
Refinement stepCycle: LAST / Resolution: 1.81→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 39 982 10759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610406
X-RAY DIFFRACTIONf_angle_d0.90714245
X-RAY DIFFRACTIONf_dihedral_angle_d16.7136244
X-RAY DIFFRACTIONf_chiral_restr0.0621536
X-RAY DIFFRACTIONf_plane_restr0.0051903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.809-1.82960.2972290.25334684X-RAY DIFFRACTION93
1.8296-1.85110.25652360.23664988X-RAY DIFFRACTION98
1.8511-1.87370.25212780.21954850X-RAY DIFFRACTION98
1.8737-1.89740.23542780.20284909X-RAY DIFFRACTION98
1.8974-1.92230.22732720.19154986X-RAY DIFFRACTION98
1.9223-1.94870.21612770.18034909X-RAY DIFFRACTION98
1.9487-1.97650.20952680.17274900X-RAY DIFFRACTION98
1.9765-2.0060.20382350.16785009X-RAY DIFFRACTION98
2.006-2.03740.19272810.16614981X-RAY DIFFRACTION98
2.0374-2.07080.20182490.16334940X-RAY DIFFRACTION99
2.0708-2.10650.20162270.1624975X-RAY DIFFRACTION99
2.1065-2.14480.19682340.16045026X-RAY DIFFRACTION99
2.1448-2.1860.19482690.15554922X-RAY DIFFRACTION99
2.186-2.23060.18312990.14894994X-RAY DIFFRACTION99
2.2306-2.27910.18452570.15054970X-RAY DIFFRACTION99
2.2791-2.33220.18842630.14944993X-RAY DIFFRACTION99
2.3322-2.39050.17862840.15144997X-RAY DIFFRACTION99
2.3905-2.45510.18552660.15724950X-RAY DIFFRACTION99
2.4551-2.52730.18622530.15725049X-RAY DIFFRACTION99
2.5273-2.60890.19012510.15745052X-RAY DIFFRACTION99
2.6089-2.70210.17672700.15475020X-RAY DIFFRACTION99
2.7021-2.81030.17692440.15765036X-RAY DIFFRACTION99
2.8103-2.93810.18242970.1495004X-RAY DIFFRACTION99
2.9381-3.0930.15112540.14225051X-RAY DIFFRACTION99
3.093-3.28670.18212620.13635060X-RAY DIFFRACTION100
3.2867-3.54030.1453180.11815002X-RAY DIFFRACTION100
3.5403-3.89640.12922600.11055103X-RAY DIFFRACTION100
3.8964-4.45950.1222930.09985057X-RAY DIFFRACTION100
4.4595-5.61620.10542970.10315094X-RAY DIFFRACTION100
5.6162-40.52070.15852900.14235168X-RAY DIFFRACTION98
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)
10.29810.1162-0.06050.3059-0.04520.08310.0177-0.1318-0.04940.1743-0.11340.0688-0.1148-0.3072-0.07950.19220.07180.03190.2285-0.05880.1464174.88527.08735.807
20.30920.0007-0.24890.1250.07820.885-0.0231-0.16410.02280.06740.01420.0039-0.20390.10570.05680.1276-0.0281-0.01930.0827-0.01140.1165197.67826.10425.283
30.13320.0389-0.08940.1433-0.00621.0609-0.0051-0.0081-0.01350.0183-0.0019-0.002-0.0422-0.097-00.08110.0065-0.00190.06870.00030.1154186.75520.119.798
40.09350.0493-0.12630.0389-0.05080.09770.02820.0503-0.0214-0.1263-0.0086-0.0701-0.04130.1500.1745-0.02560.02830.17820.02120.1534176.755-2.87737.001
50.2398-0.0317-0.14060.1763-0.01970.86820.01530.0493-0.0248-0.0357-0.0042-0.0121-0.05250.02450.00410.08150.0020.00040.0554-0.00380.1101160.977-9.77755.111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 95 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 96 THROUGH 277 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 278 THROUGH 628 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 9 THROUGH 72 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 73 THROUGH 628 )

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