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- PDB-8xg9: Crystal structure of phenylacetone monooxygenase mutant PM3 bound... -

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Basic information

Entry
Database: PDB / ID: 8xg9
TitleCrystal structure of phenylacetone monooxygenase mutant PM3 bound to FAD and NADP
ComponentsPhenylacetone monooxygenase
KeywordsOXIDOREDUCTASE / Phenylacetone Monooxygenase / FAD-binding / NADPH-binding / Monomer
Function / homology
Function and homology information


phenylacetone monooxygenase / phenylacetone monooxygenase activity / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Phenylacetone monooxygenase
Similarity search - Component
Biological speciesThermobifida fusca YX (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsLi, X. / Sun, Z.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2024
Title: Engineering of a Baeyer-Villiger monooxygenase to Improve Substrate Scope, Stereoselectivity and Regioselectivity.
Authors: Li, X. / Li, C. / Qu, G. / Yuan, B. / Sun, Z.
History
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylacetone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7116
Polymers61,8321
Non-polymers1,8785
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.249, 84.752, 92.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phenylacetone monooxygenase / PAMO / Baeyer-Villiger monooxygenase / BVMO


Mass: 61832.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca YX (bacteria) / Gene: pamO, Tfu_1490 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47PU3, phenylacetone monooxygenase

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Non-polymers , 6 types, 187 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH6.5, 0.2 M (NH4)2SO4, 30% MPEG5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Sep 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→34.98 Å / Num. obs: 44714 / % possible obs: 99.22 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 19.21
Reflection shellResolution: 2→2.073 Å / Num. unique obs: 4314 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2→34.98 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 1996 4.48 %RANDOM
Rwork0.2205 ---
obs0.2219 44594 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 123 182 4440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064378
X-RAY DIFFRACTIONf_angle_d0.8195964
X-RAY DIFFRACTIONf_dihedral_angle_d11.516599
X-RAY DIFFRACTIONf_chiral_restr0.046627
X-RAY DIFFRACTIONf_plane_restr0.005762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31891350.3042895X-RAY DIFFRACTION96
2.05-2.110.28331490.27172991X-RAY DIFFRACTION99
2.11-2.170.29991370.26513033X-RAY DIFFRACTION100
2.17-2.240.28741390.24843027X-RAY DIFFRACTION100
2.24-2.320.25011470.24663030X-RAY DIFFRACTION100
2.32-2.410.25571430.25383003X-RAY DIFFRACTION100
2.41-2.520.28031410.25743056X-RAY DIFFRACTION100
2.52-2.650.26161430.24933042X-RAY DIFFRACTION100
2.65-2.820.29081430.2563050X-RAY DIFFRACTION100
2.82-3.040.30961460.25543053X-RAY DIFFRACTION100
3.04-3.340.28271400.24233064X-RAY DIFFRACTION99
3.34-3.830.24651370.20543027X-RAY DIFFRACTION98
3.83-4.820.20091430.16893076X-RAY DIFFRACTION98
4.82-34.980.20831530.18713251X-RAY DIFFRACTION100
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)
11.61410.4168-1.22321.665-0.97913.2021-0.07870.16430.108-0.03090.07730.1401-0.0025-0.4049-0.00090.1733-0.02850.00440.2295-0.02310.242-16.361624.3796-21.3481
21.01731.931-0.93691.7709-1.82911.0646-0.30020.1288-0.1208-0.43210.1739-0.10090.2398-0.0040.1690.4056-0.04170.10880.299-0.07410.3537-10.77128.2992-28.7365
31.29580.5350.0731.6367-0.22951.06510.0405-0.17730.12470.2907-0.1129-0.0746-0.29860.11470.08480.3303-0.05980.03380.2926-0.02980.2208-10.996918.85881.0128
42.62990.29210.41292.2020.00321.39780.0544-0.0994-0.36470.3458-0.1197-0.24910.0310.13190.05250.4084-0.0889-0.06090.40880.02460.3307-5.1827.46198.7853
50.9344-0.371-0.35391.44510.25671.3453-0.0638-0.1815-0.10180.2891-0.01210.16060.03950.1160.09420.2803-0.03590.05730.2920.00550.2463-19.3395-3.39080.8221
61.15871.1432-0.48630.7609-0.50050.4858-0.247-0.0905-0.3634-0.3221-0.0694-0.34130.27170.18010.31930.40410.04490.12890.26660.04380.44480.2289.5846-26.0141
72.80080.7771-2.81840.8197-0.00285.6785-0.1305-0.2161-0.25070.0297-0.2708-0.09530.09520.08970.43290.2261-0.04150.01910.2380.03430.2913-0.828426.234-22.9134
80.5670.3061-0.24440.6854-0.95652.6152-0.1743-0.4292-0.18950.0386-0.2342-0.4730.46240.72390.46160.30360.07990.05620.55360.1020.460412.416318.1033-22.7346
90.56670.10340.22040.6106-0.3682.60580.0727-0.3121-0.1030.0876-0.1856-0.14840.12440.30090.14330.2803-0.04340.01870.45310.05340.31987.783920.2787-16.9928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 338 )
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 381 )
6X-RAY DIFFRACTION6chain 'A' and (resid 382 through 433 )
7X-RAY DIFFRACTION7chain 'A' and (resid 434 through 464 )
8X-RAY DIFFRACTION8chain 'A' and (resid 465 through 490 )
9X-RAY DIFFRACTION9chain 'A' and (resid 491 through 541 )

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