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- PDB-6sem: Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 2 -

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Basic information

Entry
Database: PDB / ID: 6sem
TitleCrystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 2
ComponentsAncestral Flavin-containing monooxygenase (FMO) 2
KeywordsMEMBRANE PROTEIN / Flavin / enzyme / Ancestral Sequence Reconstruction
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNicoll, C. / Bailleul, G. / Fiorentini, F. / Mascotti, M.L. / Fraaije, M. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
European Commission722390
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs.
Authors: Nicoll, C.R. / Bailleul, G. / Fiorentini, F. / Mascotti, M.L. / Fraaije, M.W. / Mattevi, A.
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 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
B: Ancestral Flavin-containing monooxygenase (FMO) 2
A: Ancestral Flavin-containing monooxygenase (FMO) 2
C: Ancestral Flavin-containing monooxygenase (FMO) 2
D: Ancestral Flavin-containing monooxygenase (FMO) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,8218
Polymers244,6784
Non-polymers3,1424
Water95553
1
B: Ancestral Flavin-containing monooxygenase (FMO) 2
C: Ancestral Flavin-containing monooxygenase (FMO) 2
hetero molecules


  • defined by author&software
  • Evidence: The protein has been solubilized with detergent and this means that the oligomerization state of the protein could not be seen using Gel filtration. The micelle size masks the true ...Evidence: The protein has been solubilized with detergent and this means that the oligomerization state of the protein could not be seen using Gel filtration. The micelle size masks the true oligomeric state of the protein.
  • 124 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)123,9104
Polymers122,3392
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-34 kcal/mol
Surface area43290 Å2
MethodPISA
2
A: Ancestral Flavin-containing monooxygenase (FMO) 2
D: Ancestral Flavin-containing monooxygenase (FMO) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9104
Polymers122,3392
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-32 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.961, 147.776, 144.931
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ancestral Flavin-containing monooxygenase (FMO) 2


Mass: 61169.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Due to weak electron density for residues 119 to 122, these residues have been omitted from the crystal structure
Source: (gene. exp.) synthetic construct (others) / 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 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.4 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→48.4 Å / Num. obs: 48490 / % possible obs: 93.6 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 2425 / CC1/2: 0.472 / % possible all: 76.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nmw

5nmw


Resolution: 2.8→48.4 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25581 2346 4.8 %RANDOM
Rwork0.21049 ---
obs0.21274 46144 58.31 %-
Refinement stepCycle: LAST / Resolution: 2.8→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16639 0 212 53 16904

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