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- PDB-8u42: OvsA from Halomonas utahensis, a selenoxide synthase involved in ... -

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Basic information

Entry
Database: PDB / ID: 8u42
TitleOvsA from Halomonas utahensis, a selenoxide synthase involved in ovoselenol biosynthesis
ComponentsSelenoxide synthase OvsA
KeywordsOXIDOREDUCTASE / ovoselenol / selenium / selenoxide / nonheme iron
Function / homology: / FORMIC ACID
Function and homology information
Biological speciesHalomonas utahensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIreland, K.A. / Davis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1937971 United States
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)R35-GM147557 United States
CitationJournal: Nat.Chem. / Year: 2024
Title: Discovery of the selenium-containing antioxidant ovoselenol derived from convergent evolution.
Authors: Kayrouz, C.M. / Ireland, K.A. / Ying, V.Y. / Davis, K.M. / Seyedsayamdost, M.R.
History
DepositionSep 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Selenoxide synthase OvsA
B: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,00413
Polymers109,4922
Non-polymers51211
Water12,827712
1
A: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1339
Polymers54,7461
Non-polymers3878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8714
Polymers54,7461
Non-polymers1253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.220, 115.410, 121.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Selenoxide synthase OvsA


Mass: 54745.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas utahensis (bacteria) / Strain: DSM 3051 / Gene: CK501_04640 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 723 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.58 Å3/Da / Density % sol: 65.6 % / Description: Clear hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1 M sodium acetate pH 4.8, 3.5 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→57.71 Å / Num. obs: 98747 / % possible obs: 95.18 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.07203 / Rpim(I) all: 0.07203 / Rrim(I) all: 0.1019 / Net I/σ(I): 6.57
Reflection shellResolution: 2→2.071 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.6019 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 9984 / CC1/2: 0.562 / CC star: 0.848 / Rpim(I) all: 0.6019 / Rrim(I) all: 0.8512 / % possible all: 96.39

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.4model building
MOSFLM7.4.0data reduction
Aimless0.7.7data scaling
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→57.71 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1997 2.03 %
Rwork0.1832 96356 -
obs0.1837 98353 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.78 Å2
Refinement stepCycle: LAST / Resolution: 2→57.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 27 712 7963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01387484
X-RAY DIFFRACTIONf_angle_d1.217310167
X-RAY DIFFRACTIONf_chiral_restr0.0673993
X-RAY DIFFRACTIONf_plane_restr0.0121345
X-RAY DIFFRACTIONf_dihedral_angle_d15.22882706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31661430.30386857X-RAY DIFFRACTION96.31
2.05-2.110.31881420.28226706X-RAY DIFFRACTION93.62
2.11-2.170.30731380.26296881X-RAY DIFFRACTION96.1
2.17-2.240.31851570.25046955X-RAY DIFFRACTION97.22
2.24-2.320.26931360.23466948X-RAY DIFFRACTION97.05
2.32-2.410.261400.22766964X-RAY DIFFRACTION96.9
2.41-2.520.29531400.21026924X-RAY DIFFRACTION96.27
2.52-2.650.22511440.20936677X-RAY DIFFRACTION92.97
2.65-2.820.2471400.19047001X-RAY DIFFRACTION96.81
2.82-3.040.22571380.18036950X-RAY DIFFRACTION96.2
3.04-3.340.18421460.17266810X-RAY DIFFRACTION94.22
3.34-3.830.18891420.14536833X-RAY DIFFRACTION93.65
3.83-4.820.1271490.12916925X-RAY DIFFRACTION94.42
4.82-57.710.18381420.17426925X-RAY DIFFRACTION91.09

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