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- PDB-8xg7: Crystal structure of phenylacetone monooxygenase mutant PM1 bound... -

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Basic information

Entry
Database: PDB / ID: 8xg7
TitleCrystal structure of phenylacetone monooxygenase mutant PM1 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 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)63,5014
Polymers61,9101
Non-polymers1,5913
Water3,549197
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)82.770, 85.060, 94.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 61910.223 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
#2: 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
#3: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH6.5, 0.2 M (NH4)2SO4, and 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: 1.54184 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→37.9 Å / Num. obs: 44316 / % possible obs: 97.47 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 14.48
Reflection shellResolution: 2→2.075 Å / Num. unique obs: 4090 / CC1/2: 0.666

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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→37.9 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 2013 4.54 %
Rwork0.2345 --
obs0.2362 44315 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 105 197 4517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014446
X-RAY DIFFRACTIONf_angle_d0.9786065
X-RAY DIFFRACTIONf_dihedral_angle_d9.968600
X-RAY DIFFRACTIONf_chiral_restr0.054641
X-RAY DIFFRACTIONf_plane_restr0.012780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.39381350.31872741X-RAY DIFFRACTION90
2.05-2.110.34251340.29272861X-RAY DIFFRACTION94
2.11-2.170.32411390.2962900X-RAY DIFFRACTION95
2.17-2.240.36281450.29462939X-RAY DIFFRACTION96
2.24-2.320.36651370.2882959X-RAY DIFFRACTION97
2.32-2.410.37581350.28782999X-RAY DIFFRACTION97
2.41-2.520.33241480.28573015X-RAY DIFFRACTION98
2.52-2.660.33651510.29093048X-RAY DIFFRACTION99
2.66-2.820.31371440.27423095X-RAY DIFFRACTION100
2.82-3.040.30241430.26473088X-RAY DIFFRACTION100
3.04-3.350.3141440.24893098X-RAY DIFFRACTION100
3.35-3.830.24511520.20853125X-RAY DIFFRACTION100
3.83-4.820.19931500.18153139X-RAY DIFFRACTION99
4.83-37.90.21271560.19563295X-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)
12.27490.2984-1.55321.5277-0.33583.6502-0.05980.3251-0.02830.07010.00610.14560.0275-0.57970.06290.1836-0.03080.04360.2601-0.02040.2385-14.424123.0152-24.009
21.26641.0056-0.25792.4738-0.7290.1986-0.4480.3202-0.4352-0.24160.37270.22270.4862-0.55940.02720.4373-0.12060.1760.3514-0.09940.4836-9.89929.3943-28.1204
31.13370.45240.08592.67180.06130.87880.159-0.0909-0.02720.4055-0.17-0.1535-0.19080.01920.01960.336-0.06840.05480.2646-0.0030.2475-14.864315.578-3.644
42.68180.51820.64233.09260.40482.59640.2266-0.2885-0.12640.9521-0.3914-0.5752-0.10870.29630.10430.6686-0.1834-0.1920.41290.0810.4069-2.827812.82448.9604
51.3120.6051-0.03464.79540.12440.75290.0331-0.23590.05480.8141-0.26610.0227-0.1507-0.00430.27120.4361-0.10540.04290.37820.01280.2295-17.38760.74452.8088
62.0761.995-2.60152.3317-2.12123.5182-0.1118-0.0225-0.2862-0.1247-0.065-0.14080.2130.10790.21670.3533-0.00480.11540.31030.00440.5003-13.392-1.5758-15.1514
72.50160.8038-0.79792.9199-0.85361.228-0.0511-0.2479-0.50860.0843-0.041-0.13430.43730.10920.15940.3130.00550.11710.25050.02380.46313.528313.7687-25.1278
82.44490.4964-0.44812.0121-0.93434.27380.0462-0.2108-0.29870.1794-0.2138-0.43430.13490.4720.16130.2057-0.01640.02530.23410.00640.38677.131821.0723-21.4458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 135 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 338 )
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 367 )
6X-RAY DIFFRACTION6chain 'A' and (resid 368 through 406 )
7X-RAY DIFFRACTION7chain 'A' and (resid 407 through 443 )
8X-RAY DIFFRACTION8chain 'A' and (resid 444 through 541 )

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