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- PDB-6sf0: Crystal Structure of Ancestral Flavin-containing monooxygenase (F... -

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Basic information

Entry
Database: PDB / ID: 6sf0
TitleCrystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 2 in the presence of NADP+
ComponentsAncestral Flavin-containing monooxygenase (FMO) 2
KeywordsOXIDOREDUCTASE / Flavin / enzyme / membrane protein / Ancestral Sequence Reconstruction
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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)251,30313
Polymers244,6784
Non-polymers6,6249
Water73941
1
B: Ancestral Flavin-containing monooxygenase (FMO) 2
D: Ancestral Flavin-containing monooxygenase (FMO) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9067
Polymers122,3392
Non-polymers3,5675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-36 kcal/mol
Surface area43920 Å2
MethodPISA
2
A: Ancestral Flavin-containing monooxygenase (FMO) 2
hetero molecules

C: Ancestral Flavin-containing monooxygenase (FMO) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3976
Polymers122,3392
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area11010 Å2
ΔGint-38 kcal/mol
Surface area43780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.750, 148.678, 139.119
Angle α, β, γ (deg.)90.00, 97.08, 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: Residues 119 - 122 have been omitted from the crystal structure because the electron density around these residues is extremely weak.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#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
#4: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H44O11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
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: ID23-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.01→138 Å / Num. obs: 32052 / % possible obs: 92.4 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.145 / Net I/σ(I): 5.3
Reflection shellResolution: 3.01→3.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2290 / CC1/2: 0.628 / % possible all: 64.1

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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: 3.01→138 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1573 4.9 %RANDOM
Rwork0.21056 ---
obs0.21431 30376 51.64 %-
Displacement parametersBiso mean: 97 Å2
Refinement stepCycle: LAST / Resolution: 3.01→138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17072 0 428 41 17541

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