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- PDB-7wis: Catalytic intermediate structure of N381A mutant of copper amine ... -

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Basic information

Entry
Database: PDB / ID: 7wis
TitleCatalytic intermediate structure of N381A mutant of copper amine oxidase from Arthrobacter globiformis
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / topaquinone / TPQ / amine oxidase
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 copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain
Similarity search - Domain/homology
COPPER (II) ION / PHENYLACETALDEHYDE / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMurakawa, T. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16KT0055 Japan
CitationJournal: Chem Sci / Year: 2022
Title: Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase.
Authors: Shoji, M. / Murakawa, T. / Nakanishi, S. / Boero, M. / Shigeta, Y. / Hayashi, H. / Okajima, T.
History
DepositionJan 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)138,84614
Polymers137,7412
Non-polymers1,10412
Water22,1761231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16170 Å2
ΔGint-56 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.934, 63.472, 158.100
Angle α, β, γ (deg.)90.000, 117.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-997-

HOH

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Components

#1: Protein Phenylethylamine oxidase / Primary amine oxidase / Copper amine oxidase


Mass: 68870.727 Da / Num. of mol.: 2 / Mutation: N381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / 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-HY1 / PHENYLACETALDEHYDE


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 6.8 / Details: 25 mM HEPES 1.05 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Sep 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→140.486 Å / Num. all: 130556 / Num. obs: 130556 / % possible obs: 98 % / Redundancy: 3.8 % / Rpim(I) all: 0.077 / Rrim(I) all: 0.151 / Rsym value: 0.129 / Net I/av σ(I): 3.6 / Net I/σ(I): 6.8 / Num. measured all: 492849
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-23.70.4611.669549187600.2750.5380.4612.597.1
2-2.123.70.3552.166763178590.2120.4140.3553.397.4
2.12-2.273.80.2722.763732168590.1620.3170.2724.297.9
2.27-2.453.80.2143.460168157510.1260.2490.2145.398.1
2.45-2.693.80.1654.355481145260.0980.1920.1656.798.3
2.69-33.80.1245.450587132290.0730.1440.1248.698.6
3-3.473.80.0986.144674116960.0580.1140.09810.698.7
3.47-4.253.80.0963783099430.0540.1050.0912.598.9
4.25-6.013.80.095.62900677230.0540.1050.091499
6.01-26.3593.60.0954.61505942100.060.1130.09515.796.2

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7


Resolution: 1.9→26.359 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 6384 4.89 %
Rwork0.1626 124099 -
obs0.1643 130483 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.25 Å2 / Biso mean: 30.7423 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: final / Resolution: 1.9→26.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9732 0 68 1231 11031
Biso mean--50.79 40.45 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710139
X-RAY DIFFRACTIONf_angle_d1.10513812
X-RAY DIFFRACTIONf_chiral_restr0.0481487
X-RAY DIFFRACTIONf_plane_restr0.0051834
X-RAY DIFFRACTIONf_dihedral_angle_d13.2743706
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.27131960.2503410297
1.9216-1.94420.27671990.2461407897
1.9442-1.96790.26982100.239402697
1.9679-1.99280.2782220.2309410897
1.9928-2.0190.2381840.2257408697
2.019-2.04660.27651830.2174412997
2.0466-2.07590.25332170.2095405097
2.0759-2.10680.24622190.2096412697
2.1068-2.13970.2352030.2002407097
2.1397-2.17480.23132190.1922411798
2.1748-2.21230.21762410.1875409498
2.2123-2.25250.23712250.1771410398
2.2525-2.29580.22741860.1751412898
2.2958-2.34260.18432240.1634410598
2.3426-2.39350.18982110.169411198
2.3935-2.44920.21132220.1748415298
2.4492-2.51040.24422050.1677412798
2.5104-2.57820.22032110.1699413398
2.5782-2.6540.19912270.162417198
2.654-2.73960.22212100.1624413798
2.7396-2.83740.20242310.1582411698
2.8374-2.95080.20952280.1561416998
2.9508-3.0850.17992170.1487415998
3.085-3.24730.18431980.1439420498
3.2473-3.45040.16522330.1403413398
3.4504-3.71610.15472210.1327421599
3.7161-4.08880.16452090.1315421299
4.0888-4.67760.13782250.1217422399
4.6776-5.88250.16492010.1402428899
5.8825-26.3590.20462070.1736422796
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)
10.6145-0.38420.12821.13340.15780.1480.12290.3953-0.0103-0.6272-0.1821-0.1942-0.12310.2796-0.23160.4089-0.05470.10970.56930.09980.219848.73515.17970.7888
20.3405-0.0939-0.17040.2127-0.15290.2870.07570.57730.0628-0.3841-0.124-0.0646-0.01890.0380.0190.3990.07020.04540.6202-0.01590.30732.5118-2.3551-4.3158
30.8814-0.0403-0.18690.2942-0.15850.4798-0.00620.581-0.0427-0.1298-0.06790.0522-0.1361-0.27370.07030.2720.0806-0.06430.3778-0.02340.202315.92861.0536.1048
40.5014-0.1177-0.33760.4116-0.03610.83480.05830.18280.0711-0.1249-0.0144-0.0601-0.34030.2370.06060.214-0.05540.02150.17880.03890.174838.98668.81923.1258
50.5196-0.1062-0.12150.64510.00861.44450.03090.1067-0.0276-0.0729-0.0437-0.05760.01760.2689-0.00940.08180.01410.00860.15090.00560.137437.2736-6.328226.9296
60.7295-0.13640.14530.27110.23190.26-0.0487-0.2009-0.01580.1177-0.0690.0496-0.0239-0.3759-0.05350.18670.079-0.01160.2638-0.06580.185510.99847.849569.0493
70.0769-0.0774-0.16360.04920.16030.4087-0.1127-0.26410.11960.13660.03150.01040.0586-0.1183-0.00010.18120.0083-0.0190.2401-0.00820.248220.95181.12473.5131
80.4837-0.0156-0.0970.24250.17171.1838-0.0068-0.16520.01790.07010.0301-0.042-0.21250.17170.2550.1417-0.0357-0.02260.1148-0.00280.161133.8034.535558.953
90.69330.0427-0.07680.26910.35990.55190.0211-0.07610.06180.02770.0185-0.0037-0.25630.09190.00610.2281-0.00330.01350.13410.0070.200526.71378.909748.2767
100.5806-0.0015-0.04720.42440.18951.31230.0317-0.0402-0.04470.0159-0.0483-0.00690.014-0.1131-0.00380.0958-0.0013-0.00370.09230.01190.144822.0642-5.553443.5506
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 124 )A73 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 225 )A125 - 225
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 368 )A226 - 368
5X-RAY DIFFRACTION5chain 'A' and (resid 369 through 628 )A369 - 628
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 72 )B9 - 72
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 114 )B73 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 277 )B115 - 277
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 368 )B278 - 368
10X-RAY DIFFRACTION10chain 'B' and (resid 369 through 628 )B369 - 628

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