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- PDB-6sek: Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 5 -

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Basic information

Entry
Database: PDB / ID: 6sek
TitleCrystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 5
ComponentsAncestral Flavin-containing monooxygenase 5
KeywordsOXIDOREDUCTASE / Flavin / enzyme / membrane protein / Ancestral Sequence Reconstruction
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / alpha-D-glucopyranose / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral Flavin-containing monooxygenase 5
B: Ancestral Flavin-containing monooxygenase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,12011
Polymers120,7152
Non-polymers4,4059
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-30 kcal/mol
Surface area38960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.782, 100.069, 143.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ancestral Flavin-containing monooxygenase 5


Mass: 60357.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 3 molecules

#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 33 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: PEG 4000 HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→49.9 Å / Num. obs: 38832 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4655 / CC1/2: 0.421 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29453 1964 5.1 %RANDOM
Rwork0.22224 ---
obs0.22586 36825 99.73 %-
Displacement parametersBiso mean: 84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 282 27 8329

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