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- PDB-9bxh: OvsM from Marinimicrobium koreense, a SAM-dependent N-methyltrans... -

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Basic information

Entry
Database: PDB / ID: 9bxh
TitleOvsM from Marinimicrobium koreense, a SAM-dependent N-methyltransferase involved in ovoselenol biosynthesis
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 / Putative 4-mercaptohistidine N1-methyltransferase
Function and homology information
Biological speciesMarinimicrobium koreense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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)30,1844
Polymers29,9981
Non-polymers1863
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint8 kcal/mol
Surface area11610 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

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.52 Å3/Da / Density % sol: 51.3 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 5% v/v Tacsimate, pH 7.0, 10% w/v PEG5000 MME

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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: 1.48→29 Å / Num. obs: 50394 / % possible obs: 98.86 % / Redundancy: 2 % / Biso Wilson estimate: 18.51 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02929 / Rpim(I) all: 0.02929 / Rrim(I) all: 0.04142 / Net I/σ(I): 11.38
Reflection shellResolution: 1.48→1.533 Å / Redundancy: 2 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4614 / CC1/2: 0.56 / CC star: 0.847 / Rpim(I) all: 0.679 / Rrim(I) all: 0.9602 / % possible all: 90.99

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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: MOLECULAR REPLACEMENT / Resolution: 1.48→29 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1964 1912 3.8 %
Rwork0.1764 48441 -
obs0.1772 50353 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.51 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 12 286 2153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511907
X-RAY DIFFRACTIONf_angle_d0.77622583
X-RAY DIFFRACTIONf_chiral_restr0.0731286
X-RAY DIFFRACTIONf_plane_restr0.0099340
X-RAY DIFFRACTIONf_dihedral_angle_d13.4348696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.34141190.32573126X-RAY DIFFRACTION89.59
1.52-1.560.25041380.27523332X-RAY DIFFRACTION96.47
1.56-1.60.24511250.22463414X-RAY DIFFRACTION98.77
1.6-1.660.24671390.20293460X-RAY DIFFRACTION99.81
1.66-1.710.19521340.19733478X-RAY DIFFRACTION99.92
1.71-1.780.23261430.19223445X-RAY DIFFRACTION99.94
1.78-1.860.19071320.17423502X-RAY DIFFRACTION99.97
1.86-1.960.17221360.17093452X-RAY DIFFRACTION99.89
1.96-2.090.20041290.16663486X-RAY DIFFRACTION99.97
2.09-2.250.18951470.17243490X-RAY DIFFRACTION99.97
2.25-2.470.16711390.17473516X-RAY DIFFRACTION99.97
2.47-2.830.19011410.17683514X-RAY DIFFRACTION100
2.83-3.560.18681430.17243542X-RAY DIFFRACTION100
3.57-290.19971470.15663684X-RAY DIFFRACTION99.9

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