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

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Basic information

Entry
Database: PDB / ID: 9bxj
TitleOvsM from Marinimicrobium koreense, an ovoselenol-biosynthetic N-methyltransferase in complex with SAM
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-ADENOSYLMETHIONINE / Putative 4-mercaptohistidine N1-methyltransferase
Function and homology information
Biological speciesMarinimicrobium koreense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.56 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)30,7077
Polymers29,9981
Non-polymers7096
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint13 kcal/mol
Surface area11250 Å2
Unit cell
Length a, b, c (Å)83.966, 90.566, 79.517
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

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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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.52 Å3/Da / Density % sol: 51.2 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M bicine, pH 9.0, 10% w/v PEG6000

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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: 1.56→28.87 Å / Num. obs: 43317 / % possible obs: 99.64 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.15 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03978 / Rpim(I) all: 0.03978 / Rrim(I) all: 0.05625 / Net I/σ(I): 12.4
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.6858 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 4241 / CC1/2: 0.602 / CC star: 0.867 / Rpim(I) all: 0.6858 / Rrim(I) all: 0.9698 / % possible all: 98.46

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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: 1.56→28.87 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2144 1663 3.81 %
Rwork0.1931 41978 -
obs0.1939 43317 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.32 Å2
Refinement stepCycle: LAST / Resolution: 1.56→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 47 221 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091993
X-RAY DIFFRACTIONf_angle_d1.36662701
X-RAY DIFFRACTIONf_chiral_restr0.1063300
X-RAY DIFFRACTIONf_plane_restr0.0104352
X-RAY DIFFRACTIONf_dihedral_angle_d13.7284719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.38561280.34693360X-RAY DIFFRACTION96.67
1.6-1.650.32221430.30743483X-RAY DIFFRACTION99.83
1.65-1.710.34251340.27783460X-RAY DIFFRACTION99.86
1.71-1.780.29971350.24963468X-RAY DIFFRACTION99.92
1.78-1.860.2191390.2093481X-RAY DIFFRACTION99.83
1.86-1.960.22681350.19113476X-RAY DIFFRACTION99.78
1.96-2.080.20021320.18243510X-RAY DIFFRACTION99.95
2.08-2.240.20751500.18033481X-RAY DIFFRACTION99.92
2.24-2.470.21261410.18763535X-RAY DIFFRACTION99.92
2.47-2.820.21951350.1933501X-RAY DIFFRACTION99.4
2.82-3.560.181450.1873542X-RAY DIFFRACTION99.86
3.56-28.870.18961460.16123681X-RAY DIFFRACTION99.53

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