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- PDB-2ylz: SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATI... -

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Basic information

Entry
Database: PDB / ID: 2ylz
TitleSNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE STABILIZATION: Met446Gly MUTANT
ComponentsPHENYLACETONE MONOOXYGENASE
KeywordsOXIDOREDUCTASE / OXYGENASE
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
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 / Phenylacetone monooxygenase
Similarity search - Component
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOrru, R. / Dudek, H.M. / Martinoli, C. / Torres Pazmino, D.E. / Royant, A. / Weik, M. / Fraaije, M.W. / Mattevi, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Snapshots of Enzymatic Baeyer-Villiger Catalysis: Oxygen Activation and Intermediate Stabilization.
Authors: Orru, R. / Dudek, H.M. / Martinoli, C. / Torres Pazmino, D.E. / Royant, A. / Weik, M. / Fraaije, M.W. / Mattevi, A.
History
DepositionJun 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 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)62,0954
Polymers61,1171
Non-polymers9783
Water6,089338
1
A: PHENYLACETONE MONOOXYGENASE
hetero molecules

A: PHENYLACETONE MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1908
Polymers122,2352
Non-polymers1,9556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8080 Å2
ΔGint-118.4 kcal/mol
Surface area40270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.800, 115.910, 166.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 61117.309 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 446 TO GLY

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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: 3.43 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE GROWN AT 293 K BY THE VAPOUR DIFFUSION METHOD. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 18 MG PROTEIN/ML IN 5 MM FAD AND 50 MM SODIUM PHOSPHATE PH 7.0, AND OF A ...Details: CRYSTALS WERE GROWN AT 293 K BY THE VAPOUR DIFFUSION METHOD. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 18 MG PROTEIN/ML IN 5 MM FAD AND 50 MM SODIUM PHOSPHATE PH 7.0, AND OF A WELL SOLUTION CONSISTING OF 1.5 M AMMONIUM SULPHATE AND 0.5 M LITHIUM CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 56991 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W4X

1w4x


Resolution: 2→36.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.363 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22577 2887 5.1 %RANDOM
Rwork0.18963 ---
obs0.19148 54104 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.185 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--0.17 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 63 338 4657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9636046
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23223.063222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48115681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8421540
X-RAY DIFFRACTIONr_chiral_restr0.1120.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213473
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_it1.081.52650
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96624273
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.08431785
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0374.51773
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 202 -
Rwork0.229 3950 -
obs--100 %

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