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- PDB-5zp7: Copper amine oxidase from Arthrobacter globiformis anaerobically ... -

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Basic information

Entry
Database: PDB / ID: 5zp7
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 277 K (3)
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / COPPER AMINE OXIDASE / TOPAQUINONE / TPQ
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
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 ...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: 1.631 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

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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)138,1879
Polymers137,8282
Non-polymers3597
Water17,511972
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14440 Å2
ΔGint-74 kcal/mol
Surface area41510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.730, 64.374, 158.865
Angle α, β, γ (deg.)90.000, 117.190, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1396-

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 / Copper


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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H2O

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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: 61.52 %
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: 277 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: 1.63→50 Å / Num. obs: 215558 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.94 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.046 / Rrim(I) all: 0.09 / Χ2: 2.083 / Net I/σ(I): 9.2 / Num. measured all: 834876
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.6640.775107180.7520.4390.8931.06299.6
1.66-1.6940.684107850.8010.3850.7861.11899.6
1.69-1.7240.617106670.8290.3470.711.16499.7
1.72-1.7640.531107590.8660.2990.6111.24999.7
1.76-1.7940.445107900.9090.2490.5111.34199.7
1.79-1.8440.381107400.9230.2140.4381.45899.7
1.84-1.8840.313107370.9480.1760.3611.54999.8
1.88-1.9340.261107330.9640.1470.31.68299.6
1.93-1.9940.218107640.9740.1240.2521.83699.5
1.99-2.0540.185107240.9810.1050.2131.95799.6
2.05-2.1340.168107780.9830.0950.1932.09599.4
2.13-2.213.90.143107690.9860.0820.1662.22499.4
2.21-2.313.90.128107090.9880.0740.1482.37199.2
2.31-2.433.90.119107290.9890.0690.1382.58599.3
2.43-2.593.80.114107530.990.0670.1332.94699.3
2.59-2.793.70.101108120.9910.0610.1183.39199.4
2.79-3.073.60.082108080.9920.050.0963.60899.4
3.07-3.513.60.061108540.9950.0370.0713.48199.5
3.51-4.423.50.042108680.9970.0260.0492.79499.4
4.42-503.40.034110610.9980.0210.042.5299

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7


Resolution: 1.631→39.661 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.71
RfactorNum. reflection% reflection
Rfree0.1663 10707 4.97 %
Rwork0.1487 --
obs0.1496 215374 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.35 Å2 / Biso mean: 27.5081 Å2 / Biso min: 10.99 Å2
Refinement stepCycle: final / Resolution: 1.631→39.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 16 972 10724
Biso mean--39.75 39.79 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610195
X-RAY DIFFRACTIONf_angle_d0.86913918
X-RAY DIFFRACTIONf_chiral_restr0.0611495
X-RAY DIFFRACTIONf_plane_restr0.0051855
X-RAY DIFFRACTIONf_dihedral_angle_d7.3668235
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 (%)
1.6307-1.64920.31193420.27016703704597
1.6492-1.66860.263340.24966758709299
1.6686-1.68890.23413790.235268007179100
1.6889-1.71030.25393320.231167897121100
1.7103-1.73280.23853940.222467827176100
1.7328-1.75660.24453620.207967487110100
1.7566-1.78170.21823960.201867957191100
1.7817-1.80830.20523580.191368057163100
1.8083-1.83650.22083340.18968597193100
1.8365-1.86660.20793160.185668157131100
1.8666-1.89880.19613620.174968837245100
1.8988-1.93330.19343460.16367617107100
1.9333-1.97050.18883360.15516828716499
1.9705-2.01070.17053650.1496854721999
2.0107-2.05450.18643570.146567497106100
2.0545-2.10230.17343820.14816822720499
2.1023-2.15480.15923630.14356801716499
2.1548-2.21310.1773460.14896854720099
2.2131-2.27820.1723240.14846815713999
2.2782-2.35170.17923600.14736753711399
2.3517-2.43580.15733720.14836818719099
2.4358-2.53330.17893560.15496833718999
2.5333-2.64850.16943630.15836791715499
2.6485-2.78810.18213590.1596891725099
2.7881-2.96280.1733430.15286835717899
2.9628-3.19140.16183580.150369117269100
3.1914-3.51240.15723840.13066847723199
3.5124-4.02030.13023400.11396905724599
4.0203-5.06350.12263680.10626915728399
5.0635-39.67290.13683760.14836947732398
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)
11.0504-0.0608-1.44784.8146-0.24693.285-0.00710.03580.0183-0.0508-0.01910.2058-0.0627-0.3624-0.01370.09740.02030.02870.1364-0.04230.147811.35517.600169.4934
20.34610.0316-0.03020.2170.04290.91920.0079-0.01820.00390.02840.0003-0.0059-0.07070.0107-0.00370.1229-0.0002-0.00430.080.00540.145626.6708-0.054151.0451
31.6650.719-1.12164.94840.48872.49460.06180.16870.0212-0.3092-0.1329-0.2546-0.12090.5350.01380.20310.0230.07360.33860.08070.171349.19955.16790.8735
42.5778-0.10260.09630.3872-0.11650.7280.02630.5751-0.0504-0.1853-0.034-0.02060.0102-0.02150.0040.23820.042-0.00820.3447-0.01660.164224.2929-3.9133-2.1944
50.4017-0.07960.03320.30420.01531.03390.01170.08560.0085-0.035-0.0118-0.0086-0.07750.13540.00220.1292-0.0005-0.00090.14140.00560.150736.2055-0.235125.1499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 72 )B9 - 72
2X-RAY DIFFRACTION2chain 'B' and (resid 73 through 628 )B73 - 628
3X-RAY DIFFRACTION3chain 'A' and (resid 9 through 72 )A9 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 191 )A73 - 191
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 628 )A192 - 628

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