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- PDB-2ym2: SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATI... -

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Basic information

Entry
Database: PDB / ID: 2ym2
TitleSNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE STABILIZATION: Arg337Lys MUTANT REDUCED STATE WITH NADP
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Phenylacetone monooxygenase
Similarity search - Component
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Apr 3, 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 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)62,6923
Polymers61,1631
Non-polymers1,5292
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.450, 108.450, 108.090
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 / 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 337 TO LYS

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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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: BY VAPOR-DIFFUSION AT 4 DEGREES C USING 1-3 MICROL OF PROTEIN SOLUTIONS (18 MG/ML IN 0.5 MICROM FAD AND 4 MM NADP, 50 MM TRIS/HCL PH 7.5) MIXED WITH EQUAL VOLUMES OF RESERVOIR CONTAINING 40% ...Details: BY VAPOR-DIFFUSION AT 4 DEGREES C USING 1-3 MICROL OF PROTEIN SOLUTIONS (18 MG/ML IN 0.5 MICROM FAD AND 4 MM NADP, 50 MM TRIS/HCL PH 7.5) MIXED WITH EQUAL VOLUMES OF RESERVOIR CONTAINING 40% W/V PEG4000, 100 MM MES/HCL PH 6.5, AND 100 MM NACL.

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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: 2.7→30 Å / Num. obs: 20544 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

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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 2YLR

2ylr


Resolution: 2.7→70.9 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.353 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.816 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25869 999 4.9 %RANDOM
Rwork0.20157 ---
obs0.2044 19509 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.341 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→70.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 101 55 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224438
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9756059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99123.256215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74415672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4591536
X-RAY DIFFRACTIONr_chiral_restr0.1050.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213434
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_it0.7231.52640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39824252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16931798
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6214.51807
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
Rfree0.339 81 -
Rwork0.316 1405 -
obs--99.33 %

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