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- PDB-8ux5: OvsA M401Y/Q430N/A431F from Halomonas utahensis, a hercynine-bind... -

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Basic information

Entry
Database: PDB / ID: 8ux5
TitleOvsA M401Y/Q430N/A431F from Halomonas utahensis, a hercynine-binding variant with selenoneine-biosynthetic activity
ComponentsSelenoxide synthase OvsA
KeywordsOXIDOREDUCTASE / hercynine / selenoneine / selenium / selenoxide
Function / homology:
Function and homology information
Biological speciesHalomonas utahensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsIreland, K.A. / Davis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)R35-GM147557 United States
National Science Foundation (NSF, United States)1937971 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
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 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)110,1326
Polymers109,9742
Non-polymers1584
Water54030
1
A: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0663
Polymers54,9871
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Selenoxide synthase OvsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0663
Polymers54,9871
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.174, 162.174, 124.663
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

#1: Protein Selenoxide synthase OvsA


Mass: 54987.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas utahensis (bacteria) / Strain: DSM 3051 / Production host: Escherichia coli BL21(DE3) (bacteria)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 4.45 Å3/Da / Density % sol: 72.4 % / Description: Clear hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 3.5 M sodium formate, 10 mM sarcosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.06→29.09 Å / Num. obs: 35167 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 106.98 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03673 / Rpim(I) all: 0.03673 / Rrim(I) all: 0.05194 / Net I/σ(I): 14.1
Reflection shellResolution: 3.06→3.169 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6614 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 3456 / CC1/2: 0.501 / CC star: 0.817 / Rpim(I) all: 0.6614 / Rrim(I) all: 0.9353 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CootCoot 0.9.8.7model building
XDSXDS-Apple_M1data reduction
XDSXDS-Apple_M1data scaling
PHASERPhaser 1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→29.09 Å / SU ML: 0.4654 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4876
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 1752 4.98 %
Rwork0.2028 33404 -
obs0.2053 35156 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.46 Å2
Refinement stepCycle: LAST / Resolution: 3.06→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7021 0 4 30 7055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00777268
X-RAY DIFFRACTIONf_angle_d1.10299917
X-RAY DIFFRACTIONf_chiral_restr0.0651971
X-RAY DIFFRACTIONf_plane_restr0.02171321
X-RAY DIFFRACTIONf_dihedral_angle_d17.04372538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.140.32311340.35192532X-RAY DIFFRACTION99.96
3.14-3.230.37671380.31732566X-RAY DIFFRACTION100
3.24-3.340.3751340.28862546X-RAY DIFFRACTION100
3.34-3.460.30461370.24972577X-RAY DIFFRACTION100
3.46-3.60.33071350.25212549X-RAY DIFFRACTION100
3.6-3.760.29021350.24222559X-RAY DIFFRACTION99.96
3.76-3.960.25511370.19842574X-RAY DIFFRACTION99.96
3.96-4.210.20171330.18372557X-RAY DIFFRACTION100
4.21-4.530.23851370.17432578X-RAY DIFFRACTION100
4.53-4.980.21671330.17892565X-RAY DIFFRACTION100
4.98-5.70.22911270.18892599X-RAY DIFFRACTION100
5.7-7.160.2581340.20252571X-RAY DIFFRACTION99.96
7.16-29.090.2361380.17922631X-RAY DIFFRACTION99.68

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