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- PDB-8u41: OvsA from Halomonas utahensis, an ovoselenol-biosynthetic selenox... -

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Basic information

Entry
Database: PDB / ID: 8u41
TitleOvsA from Halomonas utahensis, an ovoselenol-biosynthetic selenoxide synthase in complex with histidine
ComponentsSelenoxide synthase OvsA
KeywordsOXIDOREDUCTASE / ovoselenol / selenium / selenoxide / nonheme iron
Function / homology: / FORMIC ACID / HISTIDINE
Function and homology information
Biological speciesHalomonas utahensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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

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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)110,05410
Polymers109,4922
Non-polymers5628
Water1,53185
1
A: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0736
Polymers54,7461
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9814
Polymers54,7461
Non-polymers2353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.129, 160.129, 122.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-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, 93 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.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.26 Å3/Da / Density % sol: 71.2 % / 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, 3.9 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 18, 2023
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.72→69.34 Å / Num. obs: 47873 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 74.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02925 / Rpim(I) all: 0.02925 / Rrim(I) all: 0.04136 / Net I/σ(I): 16.89
Reflection shellResolution: 2.72→2.817 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5307 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4740 / CC1/2: 0.654 / CC star: 0.889 / Rpim(I) all: 0.5307 / Rrim(I) all: 0.7505 / % possible all: 99.92

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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: 2.72→69.34 Å / SU ML: 0.468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 1967 4.11 %
Rwork0.2247 45876 -
obs0.2256 47843 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.6 Å2
Refinement stepCycle: LAST / Resolution: 2.72→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 32 85 7285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00497454
X-RAY DIFFRACTIONf_angle_d0.877510143
X-RAY DIFFRACTIONf_chiral_restr0.0552986
X-RAY DIFFRACTIONf_plane_restr0.00961349
X-RAY DIFFRACTIONf_dihedral_angle_d17.73852661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.790.4271420.41093250X-RAY DIFFRACTION99.91
2.79-2.860.43611430.3913273X-RAY DIFFRACTION99.94
2.86-2.950.38591360.33323242X-RAY DIFFRACTION99.79
2.95-3.040.32881400.30753255X-RAY DIFFRACTION99.88
3.04-3.150.34181450.30823282X-RAY DIFFRACTION99.94
3.15-3.280.34041400.29613254X-RAY DIFFRACTION99.97
3.28-3.430.31761370.30023267X-RAY DIFFRACTION99.91
3.43-3.610.3051400.25653274X-RAY DIFFRACTION99.94
3.61-3.830.25281390.21863276X-RAY DIFFRACTION99.97
3.83-4.130.22911390.19653286X-RAY DIFFRACTION100
4.13-4.550.20611410.18293282X-RAY DIFFRACTION100
4.55-5.20.19981400.18373277X-RAY DIFFRACTION100
5.2-6.550.19851360.19663295X-RAY DIFFRACTION99.97
6.55-69.340.18971490.18863363X-RAY DIFFRACTION99.89

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