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- PDB-6se3: Crystal Structure of Ancestral Flavin-containing monooxygenase (F... -

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Entry
Database: PDB / ID: 6se3
TitleCrystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 3-6
ComponentsAncestral Flavin-containing monooxygenase (FMO) 3-6
KeywordsMEMBRANE PROTEIN / Flavin / enzyme / Ancestral Sequence Reconstruction
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXYGEN MOLECULE
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 29, 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
D: Ancestral Flavin-containing monooxygenase (FMO) 3-6
A: Ancestral Flavin-containing monooxygenase (FMO) 3-6
B: Ancestral Flavin-containing monooxygenase (FMO) 3-6
C: Ancestral Flavin-containing monooxygenase (FMO) 3-6
E: Ancestral Flavin-containing monooxygenase (FMO) 3-6
F: Ancestral Flavin-containing monooxygenase (FMO) 3-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,13424
Polymers360,7686
Non-polymers9,36618
Water6,431357
1
D: Ancestral Flavin-containing monooxygenase (FMO) 3-6
B: Ancestral Flavin-containing monooxygenase (FMO) 3-6
hetero molecules


  • defined by author&software
  • Evidence: Gel filtration was unable to clarify the oligomerization state of the enzyme due to the use of detergent during the purification. The detergent micelle masked the true oligomerization state observed.
  • 123 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)123,3788
Polymers120,2562
Non-polymers3,1226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-38 kcal/mol
Surface area42150 Å2
MethodPISA
2
A: Ancestral Flavin-containing monooxygenase (FMO) 3-6
E: Ancestral Flavin-containing monooxygenase (FMO) 3-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3788
Polymers120,2562
Non-polymers3,1226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-36 kcal/mol
Surface area42250 Å2
MethodPISA
3
C: Ancestral Flavin-containing monooxygenase (FMO) 3-6
F: Ancestral Flavin-containing monooxygenase (FMO) 3-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3788
Polymers120,2562
Non-polymers3,1226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-39 kcal/mol
Surface area42020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.089, 156.089, 370.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Ancestral Flavin-containing monooxygenase (FMO) 3-6


Mass: 60127.992 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Residues at the N and C termini were removed from the structural coordinates due to a lack of clear electron density
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.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 4000, Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→49.3 Å / Num. obs: 129389 / % possible obs: 100 % / Redundancy: 20.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.235 / Net I/σ(I): 14.3
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 2.876 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6372 / CC1/2: 0.409

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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→49.3 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.266 --Random
Rwork0.21657 ---
obs0.219 122810 99.97 %-
Displacement parametersBiso mean: 72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25188 0 618 357 26163

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