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- PDB-6y48: Baeyer-Villiger monooxygenase BVMOAFL210 from Aspergillus flavus ... -

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Basic information

Entry
Database: PDB / ID: 6y48
TitleBaeyer-Villiger monooxygenase BVMOAFL210 from Aspergillus flavus in complex with NADP
ComponentsBaeyer-Villiger monooxygenase
KeywordsFLAVOPROTEIN / Baeyer-Villiger monooxygenase
Function / homology
Function and homology information


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 / 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 / Steroid monooxygenase
Similarity search - Component
Biological speciesAspergillus flavus NRRL3357 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.087 Å
AuthorsOpperman, D.J. / Tolmie, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: Catalysts / Year: 2020
Title: Natural Variation in the ‘Control Loop’ of BVMOAFL210 and Its Influence on Regioselectivity and Sulfoxidation
Authors: Tolmie, C. / Aido-Machado, R.D. / Ferroni, F.M. / Smit, M.S. / Opperman, D.J.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baeyer-Villiger monooxygenase
B: Baeyer-Villiger monooxygenase
C: Baeyer-Villiger monooxygenase
D: Baeyer-Villiger monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,36912
Polymers257,2534
Non-polymers6,1168
Water2,954164
1
A: Baeyer-Villiger monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8423
Polymers64,3131
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baeyer-Villiger monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8423
Polymers64,3131
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Baeyer-Villiger monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8423
Polymers64,3131
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Baeyer-Villiger monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8423
Polymers64,3131
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.893, 117.311, 133.337
Angle α, β, γ (deg.)90.000, 103.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Baeyer-Villiger monooxygenase


Mass: 64313.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus NRRL3357 (mold) / Gene: AFLA_013230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8N5I0
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.5 M ammonium citrate tribasic pH 9; 27.5% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.087→129.643 Å / Num. obs: 72127 / % possible obs: 87.5 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.077 / Rrim(I) all: 0.143 / Net I/σ(I): 6.6
Reflection shellResolution: 2.087→2.361 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3606 / CC1/2: 0.62 / Rpim(I) all: 0.42 / Rrim(I) all: 0.772 / % possible all: 73.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimless0.7.1data scaling
STARANISO1.10.15data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J7X

5j7x


Resolution: 2.087→129.64 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 8.009 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 3434 4.8 %RANDOM
Rwork0.2062 ---
obs0.2088 68692 46.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.74 Å2 / Biso mean: 34.89 Å2 / Biso min: 4.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20.13 Å2
2---0.47 Å20 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2.087→129.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17366 0 404 164 17934
Biso mean--46.96 22.22 -
Num. residues----2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01318322
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716247
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.66724913
X-RAY DIFFRACTIONr_angle_other_deg1.1161.58937708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8552141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30522.153994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.581152926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.21515109
X-RAY DIFFRACTIONr_chiral_restr0.0480.22249
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024186
LS refinement shellResolution: 2.087→2.141 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.407 15 -
Rwork0.331 234 -
obs--2.16 %

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