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- PDB-8acs: Crystal structure of FMO from Janthinobacterium svalbardensis -

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Basic information

Entry
Database: PDB / ID: 8acs
TitleCrystal structure of FMO from Janthinobacterium svalbardensis
ComponentsFAD-dependent oxidoreductase
KeywordsFLAVOPROTEIN / Flavin Monooxygenase / Type II Flavin Monooxygenase / Rossmann fold / FAD / NADH / NADPH
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / FAD-dependent oxidoreductase
Function and homology information
Biological speciesJanthinobacterium svalbardensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPolidori, N. / Galuska, P. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundDOC-46 Austria
CitationJournal: Acs Catalysis / Year: 2023
Title: A Cold-Active Flavin-Dependent Monooxygenase from Janthinobacterium svalbardensis Unlocks Applications of Baeyer-Villiger Monooxygenases at Low Temperature.
Authors: Chanique, A.M. / Polidori, N. / Sovic, L. / Kracher, D. / Assil-Companioni, L. / Galuska, P. / Parra, L.P. / Gruber, K. / Kourist, R.
History
DepositionJul 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-dependent oxidoreductase
B: FAD-dependent oxidoreductase
C: FAD-dependent oxidoreductase
D: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,49124
Polymers273,8054
Non-polymers4,68620
Water4,089227
1
A: FAD-dependent oxidoreductase
C: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,33013
Polymers136,9022
Non-polymers2,42811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-dependent oxidoreductase
D: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,16011
Polymers136,9022
Non-polymers2,2589
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.302, 316.361, 65.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 134 or resid 136...
d_2ens_1(chain "B" and (resid 6 through 134 or resid 136...
d_3ens_1(chain "C" and (resid 6 through 134 or resid 136...
d_4ens_1(chain "D" and (resid 6 through 134 or resid 136...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNGLYA2 - 130
d_12ens_1ARGALAA132 - 136
d_13ens_1SERLEUA145 - 211
d_14ens_1ASPLEUA213 - 251
d_15ens_1TYRLEUA253 - 370
d_16ens_1ASPLEUA372 - 443
d_17ens_1METSERA445 - 598
d_18ens_1FADFADB
d_21ens_1ASNGLYF1 - 129
d_22ens_1ARGLEUF131 - 202
d_23ens_1ASPLEUF204 - 242
d_24ens_1TYRLEUF244 - 361
d_25ens_1ASPLEUF363 - 434
d_26ens_1METSERF436 - 589
d_27ens_1FADFADG
d_31ens_1ASNGLYM1 - 129
d_32ens_1ARGALAM131 - 135
d_33ens_1SERLEUM138 - 204
d_34ens_1ASPLEUM206 - 244
d_35ens_1TYRLEUM246 - 363
d_36ens_1ASPLEUM365 - 436
d_37ens_1METSERM438 - 591
d_38ens_1FADFADN
d_41ens_1ASNGLYT1 - 129
d_42ens_1ARGALAT131 - 135
d_43ens_1SERLEUT144 - 210
d_44ens_1ASPLEUT212 - 250
d_45ens_1TYRLEUT252 - 369
d_46ens_1ASPLEUT371 - 442
d_47ens_1METSERT444 - 597
d_48ens_1FADFADU

NCS oper:
IDCodeMatrixVector
1given(-0.491575078935, 0.658330887702, -0.570047703327), (0.656230636832, 0.710355191252, 0.254473679473), (0.572464228624, -0.248989848305, -0.781209806894)116.602138816, 41.4578619522, 39.6270446864
2given(0.512047815977, -0.621516782817, 0.592894529263), (-0.62538976756, -0.742916384001, -0.238668986285), (0.588807840288, -0.248580238675, -0.769098948222)-47.382998634, -46.7084654797, 71.7369436926
3given(-0.999415457284, -0.0340613560266, -0.00292707484417), (0.0340889769712, -0.999369064279, -0.00997070770099), (-0.00258561222325, -0.0100646603834, 0.999946007153)67.8819028756, -2.11860425411, -32.8996928288

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Components

#1: Protein
FAD-dependent oxidoreductase


Mass: 68451.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium svalbardensis (bacteria)
Gene: CNX70_19775 / Plasmid: pET-28a(+)-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A290WZ30
#2: Chemical
ChemComp-FAD / 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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallophore LuXo4, 14% PEG 8000, 17.5% Glycerol, 100 mM BIS-TRIS buffer (pH 6.5).
Temp details: The crystals were grown inside a cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.34024 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2021
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34024 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 92245 / % possible obs: 88.98 % / Redundancy: 13.5 % / Biso Wilson estimate: 45.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09469 / Rpim(I) all: 0.02649 / Rrim(I) all: 0.09841 / Net I/σ(I): 20.01
Reflection shellResolution: 2.5→2.591 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.7708 / Num. unique obs: 10156 / CC1/2: 0.922 / CC star: 0.98 / Rpim(I) all: 0.2143 / Rrim(I) all: 0.8006 / % possible all: 99.3

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
PHENIX19refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Model

Resolution: 2.5→49.44 Å / SU ML: 0.3672 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 4607 5 %
Rwork0.182 87565 -
obs0.1844 92172 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.87 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18467 0 313 227 19007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009119292
X-RAY DIFFRACTIONf_angle_d1.055726151
X-RAY DIFFRACTIONf_chiral_restr0.05722753
X-RAY DIFFRACTIONf_plane_restr0.00883358
X-RAY DIFFRACTIONf_dihedral_angle_d14.88766979
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.678445978358
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.626037626729
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.889937044935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.38181830.28713193X-RAY DIFFRACTION98.17
2.53-2.560.40521700.26313194X-RAY DIFFRACTION99.79
2.56-2.590.30171570.25923252X-RAY DIFFRACTION99.97
2.59-2.620.3651820.2473251X-RAY DIFFRACTION99.91
2.62-2.640.345860.25721663X-RAY DIFFRACTION96.1
2.7-2.730.29311210.2382661X-RAY DIFFRACTION98.97
2.73-2.770.31511620.22793182X-RAY DIFFRACTION99.49
2.77-2.820.30471550.23863203X-RAY DIFFRACTION98.56
2.82-2.860.29291570.23433178X-RAY DIFFRACTION96.5
2.86-2.910.29421700.23733129X-RAY DIFFRACTION97.4
2.91-2.970.33262000.25653240X-RAY DIFFRACTION99.71
2.97-3.020.33461690.24843220X-RAY DIFFRACTION99.76
3.02-3.080.32051470.23393256X-RAY DIFFRACTION99.68
3.08-3.150.27711710.21613264X-RAY DIFFRACTION99.71
3.15-3.220.24391650.20853230X-RAY DIFFRACTION99.65
3.22-3.30.25141850.20333252X-RAY DIFFRACTION99.97
3.31-3.390.29411710.22073254X-RAY DIFFRACTION99.48
3.39-3.490.2757660.22091225X-RAY DIFFRACTION37.62
3.49-3.610.25881620.21743275X-RAY DIFFRACTION99.88
3.61-3.740.2471970.20221770X-RAY DIFFRACTION53.99
3.74-3.870.21281460.16943008X-RAY DIFFRACTION99.43
3.93-4.060.22011380.15572347X-RAY DIFFRACTION99.24
4.06-4.280.18041860.14753266X-RAY DIFFRACTION100
4.28-4.540.17491860.13273284X-RAY DIFFRACTION99.94
4.54-4.890.16151690.12513354X-RAY DIFFRACTION100
4.89-5.390.16351690.13223173X-RAY DIFFRACTION95.49
5.39-6.160.18681920.15223289X-RAY DIFFRACTION98.84
6.16-7.760.19731500.16083428X-RAY DIFFRACTION99.94
7.76-49.440.15621950.14223524X-RAY DIFFRACTION98.62

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