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- PDB-4ovi: Phenylacetone monooxygenase: oxidised enzyme in complex with APADP -

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Basic information

Entry
Database: PDB / ID: 4ovi
TitlePhenylacetone monooxygenase: oxidised enzyme in complex with APADP
ComponentsPhenylacetone monooxygenase
KeywordsOXIDOREDUCTASE / flavin / cofactor / Baeyer-Villiger
Function / homology
Function and homology information


phenylacetone monooxygenase / phenylacetone monooxygenase activity / N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase / : / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Phenylacetone monooxygenase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMartinoli, C. / Fraaije, M.W. / Mattevi, A.
Funding supportEU, Italy, 2items
OrganizationGrant numberCountry
FP7212281EU
Fondazione CARIPLO2008.3148 Italy
CitationJournal: Acs Catalysis / Year: 2013
Title: Beyond the Protein Matrix: Probing Cofactor Variants in a Baeyer-Villiger Oxygenation Reaction.
Authors: Martinoli, C. / Dudek, H.M. / Orru, R. / Edmondson, D.E. / Fraaije, M.W. / Mattevi, A.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist / struct_keywords / symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.pdbx_keywords / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylacetone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0537
Polymers61,1911
Non-polymers1,8626
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.238, 107.238, 107.135
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 61191.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: pamO / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q47PU3, phenylacetone monooxygenase

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Non-polymers , 7 types, 220 molecules

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


Mass: 785.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-N01 / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE


Mass: 739.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H26N6O17P3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG4000 40% w/v, MES 100 mM, NaCl 100 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 59226 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 0.146
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLS

2yls


Resolution: 1.87→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.327 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27698 3033 5.1 %RANDOM
Rwork0.22102 ---
obs0.22382 56153 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.41 Å20 Å2
2--0.41 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 1.87→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 122 214 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194476
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.9776109
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10623.211218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95415675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6691537
X-RAY DIFFRACTIONr_chiral_restr0.1360.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213479
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5472.7392128
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.294.0932658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3373.0082347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.70924.4047281
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 215 -
Rwork0.347 4150 -
obs--100 %
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)
10.97530.18510.26460.72220.25541.4237-0.0283-0.0824-0.0601-0.0743-0.13980.2565-0.0142-0.26250.1680.06840.0174-0.06890.0626-0.06690.163930.5462-22.593615.0278
20.54540.03340.55031.53340.47541.29140.030.0659-0.0656-0.07520.0244-0.03580.00290.2955-0.05430.10660.0145-0.02160.0919-0.00210.042456.9923-23.037916.1021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 158
2X-RAY DIFFRACTION1A390 - 701
3X-RAY DIFFRACTION2A169 - 389

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