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- PDB-6wpu: Structure of S-allyl-L-cysteine S-oxygenase from Allium sativum -

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Basic information

Entry
Database: PDB / ID: 6wpu
TitleStructure of S-allyl-L-cysteine S-oxygenase from Allium sativum
ComponentsFlavin-containing monooxygenase
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / FLAVIN-CONTAINING MONOOXYGENASE
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / Oxidoreductases / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-containing monooxygenase
Similarity search - Component
Biological speciesAllium sativum (garlic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.084 Å
AuthorsTanner, J.J. / Campbell, A.C. / Schuermann, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2003658 United States
National Science Foundation (NSF, United States)CHE-2003986 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure and function of a flavin-dependent S-monooxygenase from garlic (Allium sativum).
Authors: Valentino, H. / Campbell, A.C. / Schuermann, J.P. / Sultana, N. / Nam, H.G. / LeBlanc, S. / Tanner, J.J. / Sobrado, P.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1788
Polymers51,8171
Non-polymers1,3627
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.717, 139.717, 77.873
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

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Components

#1: Protein Flavin-containing monooxygenase / S-allyl-L-cysteine S-oxygenase


Mass: 51816.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allium sativum (garlic) / Gene: AsFMO1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4U3V7, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.7 M ammonium sulfate, 0.1 M HEPES pH 7.5, and 0.0025 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.08→121 Å / Num. obs: 101059 / % possible obs: 99.7 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.039 / Rrim(I) all: 0.132 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.08-2.149.81.6733845239050.6420.5551.7651.696.7
9.08-1219.70.0368687060.9990.010.03260.7100

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.084→120.998 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 22.32
RfactorNum. reflection% reflection
Rfree0.2037 5068 5.01 %
Rwork0.1782 --
obs0.1796 101059 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.6 Å2 / Biso mean: 47.4604 Å2 / Biso min: 21.87 Å2
Refinement stepCycle: final / Resolution: 2.084→120.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 83 157 3713
Biso mean--47.46 47.23 -
Num. residues----439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0842-2.10780.39191350.333278686
2.1078-2.13260.28991480.29453300100
2.1326-2.15870.33271680.28313188100
2.1587-2.1860.30161820.26793169100
2.186-2.21480.28151280.25693299100
2.2148-2.24510.28531780.25693166100
2.2451-2.27720.25871480.24193253100
2.2772-2.31120.28321480.24043210100
2.3112-2.34730.2311420.24213253100
2.3473-2.38580.3161700.2283187100
2.3858-2.42690.27032130.22813178100
2.4269-2.4710.23772120.21133153100
2.471-2.51860.25491720.21463237100
2.5186-2.570.24791900.21443230100
2.57-2.62590.28481160.21383224100
2.6259-2.6870.23791520.20413268100
2.687-2.75420.25661960.19383175100
2.7542-2.82860.21851500.19343206100
2.8286-2.91190.20221630.19463251100
2.9119-3.00590.26271300.19653211100
3.0059-3.11330.25621680.18863235100
3.1133-3.2380.22482080.1823185100
3.238-3.38540.19431780.17543206100
3.3854-3.56380.16271320.15913248100
3.5638-3.78710.16631700.14983228100
3.7871-4.07960.18492000.13643154100
4.0796-4.49010.14892030.12853188100
4.4901-5.13990.14442260.1363190100
5.1399-6.47570.18341700.16463198100
6.4757-120.9980.18681720.1643215100
Refinement TLS params.Method: refined / Origin x: -48.7978 Å / Origin y: 48.8023 Å / Origin z: 30.7476 Å
111213212223313233
T0.1924 Å2-0.0467 Å2-0.0036 Å2-0.3839 Å2-0.0306 Å2--0.326 Å2
L0.7157 °20.2325 °2-0.0217 °2-0.6816 °2-0.658 °2--2.9203 °2
S-0.038 Å °-0.0037 Å °0.0182 Å °-0.0266 Å °0.1189 Å °0.1049 Å °0.0652 Å °-0.5586 Å °-0.0584 Å °
Refinement TLS groupSelection details: chain 'A'

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