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- PDB-8xg8: Crystal structure of phenylacetone monooxygenase mutant PM2 bound... -

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Basic information

Entry
Database: PDB / ID: 8xg8
TitleCrystal structure of phenylacetone monooxygenase mutant PM2 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 / MOLECULAR REPLACEMENT / Resolution: 2.13 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)63,8367
Polymers61,9561
Non-polymers1,8796
Water3,891216
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)81.853, 84.710, 91.714
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: 61956.316 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 , 5 types, 222 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
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: Oct 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→40.01 Å / Num. obs: 34399 / % possible obs: 94.58 % / Redundancy: 13 % / CC1/2: 0.998 / Net I/σ(I): 15.97
Reflection shellResolution: 2.13→2.206 Å / Num. unique obs: 3067 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→40.01 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1726 5.02 %
Rwork0.2166 --
obs0.2192 34383 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 120 216 4498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034409
X-RAY DIFFRACTIONf_angle_d0.536015
X-RAY DIFFRACTIONf_dihedral_angle_d8.977596
X-RAY DIFFRACTIONf_chiral_restr0.041634
X-RAY DIFFRACTIONf_plane_restr0.004772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.190.33711280.28342436X-RAY DIFFRACTION86
2.19-2.260.35181250.28432488X-RAY DIFFRACTION87
2.26-2.340.35041350.2762505X-RAY DIFFRACTION89
2.34-2.440.30011400.26472556X-RAY DIFFRACTION91
2.44-2.550.34011320.26952634X-RAY DIFFRACTION92
2.55-2.680.27611420.26062722X-RAY DIFFRACTION96
2.68-2.850.33881500.25262834X-RAY DIFFRACTION99
2.85-3.070.30711530.2262846X-RAY DIFFRACTION100
3.07-3.380.25121540.21912881X-RAY DIFFRACTION100
3.38-3.870.25951480.1882885X-RAY DIFFRACTION100
3.87-4.870.22841570.16782830X-RAY DIFFRACTION97
4.87-40.010.21081620.1863040X-RAY DIFFRACTION99
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)
11.28820.6822-0.79861.0107-0.93391.4724-0.12360.2936-0.1363-0.02640.03450.0620.1652-0.36030.01610.1835-0.07140.05930.2352-0.06720.2506-13.554320.8257-24.5859
21.03850.6646-0.12082.468-0.00110.27040.156-0.2098-0.12140.5807-0.1971-0.1542-0.05970.06360.03250.3533-0.08410.02450.2336-0.00420.204-12.549810.54780.8863
31.6276-0.0885-0.47770.74880.17782.802-0.0709-0.0625-0.24810.1531-0.1228-0.34970.2080.23690.17590.2097-0.02130.07230.17710.03960.38175.553418.7412-22.7947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 163 )
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 393 )
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 541 )

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