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- PDB-4c77: Phenylacetone monooxygenase: oxidised R337K mutant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4c77
TitlePhenylacetone monooxygenase: oxidised R337K mutant in complex with APADP
ComponentsPHENYLACETONE MONOOXYGENASE
KeywordsOXIDOREDUCTASE / FLAVIN / 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
FLAVIN-ADENINE DINUCLEOTIDE / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE / Phenylacetone monooxygenase
Similarity search - Component
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMartinoli, C. / Fraaije, M.W. / Mattevi, A.
CitationJournal: Acs Catal. / 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: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)62,9714
Polymers61,1631
Non-polymers1,8073
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.360, 107.360, 106.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PHENYLACETONE MONOOXYGENASE / PAMO / BAEYER-VILLIGER MONOOXYGENASE / BVMO


Mass: 61163.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Plasmid: PBAD / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): TOP10 / References: UniProt: Q47PU3, phenylacetone monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-N01 / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE


Mass: 739.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N6O17P3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14 / Wavelength: 1.0068
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0068 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19765 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YLS

2yls


Resolution: 2.7→35.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.565 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 1.044 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 960 4.9 %RANDOM
Rwork0.19322 ---
obs0.19629 18788 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å21.03 Å20 Å2
2--1.03 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 111 32 4369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194505
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9766154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9155542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59723.063222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9715689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9731540
X-RAY DIFFRACTIONr_chiral_restr0.1120.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213510
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_it2.8284.0932135
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.326.1392670
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5344.2352369
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 74 -
Rwork0.326 1360 -
obs--99.24 %

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