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- PDB-7yj0: Structural basis of oxepinone formation by a flavin-monooxygenase VibO -

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Basic information

Entry
Database: PDB / ID: 7yj0
TitleStructural basis of oxepinone formation by a flavin-monooxygenase VibO
ComponentsVibO
KeywordsOXIDOREDUCTASE / Monooxygenase / Ring-expansive oxygenation
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesBoreostereum vibrans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsZhang, M.F. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977101; 21822705 China
CitationJournal: Nat Commun / Year: 2023
Title: A flavin-monooxygenase catalyzing oxepinone formation and the complete biosynthesis of vibralactone.
Authors: Feng, K.N. / Zhang, Y. / Zhang, M. / Yang, Y.L. / Liu, J.K. / Pan, L. / Zeng, Y.
History
DepositionJul 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VibO
B: VibO
C: VibO
D: VibO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,4959
Polymers287,2614
Non-polymers3,2345
Water7,999444
1
A: VibO
B: VibO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,2014
Polymers143,6302
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-19 kcal/mol
Surface area43620 Å2
MethodPISA
2
C: VibO
D: VibO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,2935
Polymers143,6302
Non-polymers1,6633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-23 kcal/mol
Surface area43280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.083, 92.504, 104.639
Angle α, β, γ (deg.)89.874, 74.919, 75.746
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
VibO


Mass: 71815.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Boreostereum vibrans (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.425→71.979 Å / Num. obs: 94891 / % possible obs: 92.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 42.67 Å2 / CC1/2: 0.995 / Net I/σ(I): 6
Reflection shellResolution: 2.425→2.467 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4814 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→34.38 Å / SU ML: 0.3162 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.0521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 4737 5 %
Rwork0.1762 90097 -
obs0.1789 94834 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.12 Å2
Refinement stepCycle: LAST / Resolution: 2.43→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19255 0 218 444 19917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010420012
X-RAY DIFFRACTIONf_angle_d1.147527266
X-RAY DIFFRACTIONf_chiral_restr0.06813010
X-RAY DIFFRACTIONf_plane_restr0.00713504
X-RAY DIFFRACTIONf_dihedral_angle_d16.1337089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.450.31231810.24713069X-RAY DIFFRACTION95.03
2.45-2.480.30881490.25363075X-RAY DIFFRACTION94.82
2.48-2.510.31241640.23813054X-RAY DIFFRACTION95.18
2.51-2.540.29651660.24453086X-RAY DIFFRACTION94.73
2.54-2.580.33131800.2463064X-RAY DIFFRACTION94.44
2.58-2.610.31361420.24673053X-RAY DIFFRACTION94.78
2.61-2.650.36131510.23743086X-RAY DIFFRACTION94.98
2.65-2.690.30011370.2253133X-RAY DIFFRACTION94.59
2.69-2.730.24661580.21293014X-RAY DIFFRACTION94.15
2.73-2.780.30241590.22213029X-RAY DIFFRACTION94.6
2.78-2.820.28031510.22623097X-RAY DIFFRACTION94.09
2.82-2.880.29311590.22032999X-RAY DIFFRACTION93.49
2.88-2.930.31421730.21972981X-RAY DIFFRACTION93.01
2.93-2.990.26571790.21683060X-RAY DIFFRACTION93.13
2.99-3.060.27641650.21252969X-RAY DIFFRACTION92.53
3.06-3.130.27551530.20512951X-RAY DIFFRACTION91.46
3.13-3.20.25511570.20332954X-RAY DIFFRACTION90.86
3.2-3.290.26271510.20062854X-RAY DIFFRACTION88.77
3.29-3.390.281630.19982735X-RAY DIFFRACTION85.06
3.39-3.50.22611260.19012579X-RAY DIFFRACTION78.36
3.5-3.620.23761460.18083063X-RAY DIFFRACTION95.28
3.62-3.770.22651540.17283087X-RAY DIFFRACTION95.66
3.77-3.940.2111800.16213082X-RAY DIFFRACTION95.6
3.94-4.150.21241700.14643102X-RAY DIFFRACTION95.48
4.15-4.40.1821730.13843087X-RAY DIFFRACTION95.41
4.4-4.740.18311530.12613024X-RAY DIFFRACTION93.58
4.74-5.220.1811500.13933025X-RAY DIFFRACTION92.94
5.22-5.970.1761440.15092929X-RAY DIFFRACTION90.41
5.97-7.510.17641330.15762711X-RAY DIFFRACTION83.11
7.51-34.380.17031700.13373145X-RAY DIFFRACTION97.39

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