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- PDB-5j7x: Baeyer-Villiger monooxygenase BVMOAFL838 from Aspergillus flavus -

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Basic information

Entry
Database: PDB / ID: 5j7x
TitleBaeyer-Villiger monooxygenase BVMOAFL838 from Aspergillus flavus
ComponentsDimethylaniline monooxygenase, putative
KeywordsOXIDOREDUCTASE / Baeyer-Villiger monooxygenase
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding / membrane => GO:0016020
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 / Dimethylaniline monooxygenase, putative
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFerroni, F.M. / Tolmie, C. / Smit, M.S. / Opperman, D.J.
CitationJournal: Plos One / Year: 2016
Title: Structural and Catalytic Characterization of a Fungal Baeyer-Villiger Monooxygenase.
Authors: Ferroni, F.M. / Tolmie, C. / Smit, M.S. / Opperman, D.J.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Dimethylaniline monooxygenase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2874
Polymers62,2421
Non-polymers1,0453
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-23 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.670, 177.510, 76.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Dimethylaniline monooxygenase, putative


Mass: 62241.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: AFLA_016370 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8N653
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 9 / Details: 0.1 M Tris-HCl pH 9, 1.8 M ammonium sulphate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.9→32.4 Å / Num. obs: 58733 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.081 / Net I/av σ(I): 8.288 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-26.30.6691.1199.6
2-2.126.30.4051.8199.7
2.12-2.275.50.2493199.5
2.27-2.456.60.184.1199.8
2.45-2.696.60.1256199.9
2.69-36.40.0891100
3-3.475.50.0513.7199.1
3.47-4.256.70.03817.21100
4.25-6.0160.03418.5199.5
6.01-32.4196.30.02822.4198

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.54 Å32.42 Å
Translation7.54 Å32.42 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
REFMAC5refinement
PDB_EXTRACT3.2data extraction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W4X

1w4x


Resolution: 1.9→32.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.275 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 2981 5.1 %RANDOM
Rwork0.1571 ---
obs0.1594 55752 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.49 Å2 / Biso mean: 28.445 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.9→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 69 361 4648
Biso mean--24.05 36.08 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0194419
X-RAY DIFFRACTIONr_bond_other_d0.0030.024061
X-RAY DIFFRACTIONr_angle_refined_deg2.7071.9596015
X-RAY DIFFRACTIONr_angle_other_deg1.27839349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24424.151212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97315705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3271524
X-RAY DIFFRACTIONr_chiral_restr0.2030.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0214989
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021056
X-RAY DIFFRACTIONr_mcbond_it1.9561.9172112
X-RAY DIFFRACTIONr_mcbond_other1.9531.9162110
X-RAY DIFFRACTIONr_mcangle_it2.8542.8592637
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 211 -
Rwork0.24 4074 -
all-4285 -
obs--99.33 %
Refinement TLS params.Method: refined / Origin x: 131.243 Å / Origin y: 196.1817 Å / Origin z: 31.3771 Å
111213212223313233
T0.0425 Å2-0.013 Å2-0.0071 Å2-0.0095 Å20.0082 Å2--0.0351 Å2
L0.8679 °2-0.1307 °20.1475 °2-0.2423 °2-0.0934 °2--0.5067 °2
S-0.0243 Å °-0.0158 Å °0.1192 Å °-0.0591 Å °-0.003 Å °-0.0582 Å °-0.0197 Å °0.0186 Å °0.0273 Å °

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