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- PDB-7al4: Ancestral Flavin-containing monooxygenase (FMO) 1 (mammalian) -

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Basic information

Entry
Database: PDB / ID: 7al4
TitleAncestral Flavin-containing monooxygenase (FMO) 1 (mammalian)
ComponentsAncestral Flavin-containing monooxygenase 1 (mammalian)
KeywordsFLAVOPROTEIN / FMO Paired Rossman fold Xenobiotic detoxification
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNicoll, C.R. / Mattevi, A.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission722390European Union
H2020 Marie Curie Actions of the European Commission847675European Union
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Ancestral reconstruction of mammalian FMO1 enables structural determination, revealing unique features that explain its catalytic properties.
Authors: Bailleul, G. / Nicoll, C.R. / Mascotti, M.L. / Mattevi, A. / Fraaije, M.W.
History
DepositionOct 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Ancestral Flavin-containing monooxygenase 1 (mammalian)
C: Ancestral Flavin-containing monooxygenase 1 (mammalian)
B: Ancestral Flavin-containing monooxygenase 1 (mammalian)
A: Ancestral Flavin-containing monooxygenase 1 (mammalian)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,80723
Polymers239,3374
Non-polymers9,47019
Water72140
1
D: Ancestral Flavin-containing monooxygenase 1 (mammalian)
A: Ancestral Flavin-containing monooxygenase 1 (mammalian)
hetero molecules


  • defined by author
  • Evidence: Gel filtration could not conclude whether the protein was dimerized due to the presence of detergent in solution that masks the actual protein oligomerization state. In other words, it ...Evidence: Gel filtration could not conclude whether the protein was dimerized due to the presence of detergent in solution that masks the actual protein oligomerization state. In other words, it increases the overall size of the oligomeric state.
  • 125 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)125,02414
Polymers119,6682
Non-polymers5,35512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ancestral Flavin-containing monooxygenase 1 (mammalian)
B: Ancestral Flavin-containing monooxygenase 1 (mammalian)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7839
Polymers119,6682
Non-polymers4,1157
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.919, 92.453, 156.688
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
31B
41A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111D3 - 540
2111C3 - 540
3111B3 - 540
4111A3 - 540

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.315001, -0.410436, 0.855755), (-0.503307, -0.836672, -0.216017), (0.804647, -0.362661, -0.470128)-52.6248, -77.32368, 28.21989
3given(0.59129, -0.748568, -0.300037), (0.789951, 0.462719, 0.402329), (-0.162338, -0.474908, 0.864933)-22.30702, 73.61282, -81.81219
4given(0.223445, 0.422587, 0.878347), (0.393704, -0.863479, 0.315278), (0.891667, 0.275361, -0.359315)-5.4223, 20.72189, -1.67432

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Components

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Protein / Sugars , 2 types, 10 molecules DCBA

#1: Protein
Ancestral Flavin-containing monooxygenase 1 (mammalian)


Mass: 59834.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: FMO1 / Production host: Escherichia coli (E. coli) / References: flavin-containing monooxygenase
#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 53 molecules

#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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES (pH 7.5), PEG 4000 (10% v/v) and glycerol (20% v/v)
PH range: 7.2-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 3→49.1 Å / Num. obs: 39983 / % possible obs: 60.2 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.245 / Net I/σ(I): 5.5
Reflection shellResolution: 3→3.041 Å / Redundancy: 5 % / Rmerge(I) obs: 7.993 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 567 / CC1/2: 0.028 / % possible all: 14.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SE3

6se3


Resolution: 3→49.1 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.856 / SU B: 22.644 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.624 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 817 2 %RANDOM
Rwork0.22841 ---
obs0.22913 39119 60.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.326 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20.78 Å2
2---0.32 Å20 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 3→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16410 0 629 40 17079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01317498
X-RAY DIFFRACTIONr_bond_other_d0.0040.01716179
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.68123832
X-RAY DIFFRACTIONr_angle_other_deg1.1181.60137650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19352073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92122.405790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.174152818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2691584
X-RAY DIFFRACTIONr_chiral_restr0.0510.22336
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218880
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023620
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_it4.668.6528325
X-RAY DIFFRACTIONr_mcbond_other4.668.6528324
X-RAY DIFFRACTIONr_mcangle_it7.7312.96310387
X-RAY DIFFRACTIONr_mcangle_other7.7312.96410388
X-RAY DIFFRACTIONr_scbond_it4.068.8459173
X-RAY DIFFRACTIONr_scbond_other4.0598.8459174
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.02613.18313446
X-RAY DIFFRACTIONr_long_range_B_refined11.6599.72319614
X-RAY DIFFRACTIONr_long_range_B_other11.6599.72419615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 7835 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
D29.85
C52.04
B11.79
A23.08
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 11 -
Rwork0.386 685 -
obs--14.14 %

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