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- PDB-9bxk: OvsM from Marinimicrobium koreense, an ovoselenol-biosynthetic N-... -

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Basic information

Entry
Database: PDB / ID: 9bxk
TitleOvsM from Marinimicrobium koreense, an ovoselenol-biosynthetic N-methyltransferase in complex with 5-selenohistidine and SAH
Components5-selenohistidine N-methyltransferase OvsM
KeywordsTRANSFERASE / ovoselenol / 5-selenohistidine / S-adenosyl-L-methionine / N-methyltransferase
Function / homologyPutative 4-mercaptohistidine N1-methyltranferase, OvoA C-terminal domain / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / : / S-ADENOSYL-L-HOMOCYSTEINE / Putative 4-mercaptohistidine N1-methyltransferase
Function and homology information
Biological speciesMarinimicrobium koreense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.66 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/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
CitationJournal: Structure / Year: 2025
Title: Structural and functional analysis of SAM-dependent N-methyltransferases involved in ovoselenol and ovothiol biosynthesis.
Authors: Ireland, K.A. / Kayrouz, C.M. / Abbott, M.L. / Seyedsayamdost, M.R. / Davis, K.M.
History
DepositionMay 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: 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.year / _citation_author.identifier_ORCID
Revision 1.2Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-selenohistidine N-methyltransferase OvsM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6784
Polymers29,9981
Non-polymers6813
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint4 kcal/mol
Surface area11310 Å2
Unit cell
Length a, b, c (Å)83.838, 90.058, 80.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein 5-selenohistidine N-methyltransferase OvsM


Mass: 29997.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinimicrobium koreense (bacteria) / Strain: DSM 16974 / Gene: EDC38_1804 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3N1P0S2
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1AS0 / 5-selanyl-L-histidine


Type: L-peptide linking / Mass: 234.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3O2Se / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M tri-sodium citrate, 30% v/v PEG400

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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: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.66→29 Å / Num. obs: 35794 / % possible obs: 98.75 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.26 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05334 / Rpim(I) all: 0.05334 / Rrim(I) all: 0.07543 / Net I/σ(I): 9.95
Reflection shellResolution: 1.66→1.719 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.6965 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3373 / CC1/2: 0.521 / CC star: 0.827 / Rpim(I) all: 0.6965 / Rrim(I) all: 0.985 / % possible all: 95.33

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Processing

Software
NameVersionClassification
XDSXDS-Apple_M1data reduction
XDSXDS-Apple_M1data scaling
PHASER1.20.1_4487phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SIR / Resolution: 1.66→29 Å / SU ML: 0.2028 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 1362 3.81 %
Rwork0.1777 34405 -
obs0.1787 35767 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.79 Å2
Refinement stepCycle: LAST / Resolution: 1.66→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 42 282 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132000
X-RAY DIFFRACTIONf_angle_d1.20662719
X-RAY DIFFRACTIONf_chiral_restr0.0714302
X-RAY DIFFRACTIONf_plane_restr0.0349356
X-RAY DIFFRACTIONf_dihedral_angle_d14.0392734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.720.35821300.3073237X-RAY DIFFRACTION95.36
1.72-1.790.31641310.27273429X-RAY DIFFRACTION98.94
1.79-1.870.25091330.22443424X-RAY DIFFRACTION99.08
1.87-1.970.23851360.20253397X-RAY DIFFRACTION99.02
1.97-2.090.20741280.17643449X-RAY DIFFRACTION99.47
2.09-2.250.20471470.17823442X-RAY DIFFRACTION99.64
2.25-2.480.20151390.17683477X-RAY DIFFRACTION99.7
2.48-2.840.21731360.17593486X-RAY DIFFRACTION99.86
2.84-3.570.18821420.16823519X-RAY DIFFRACTION99.84
3.57-290.16971400.14893545X-RAY DIFFRACTION96.97

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