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- PDB-9bxl: OvoM from Sulfuricurvum sp. isolate STB_99, an ovothiol-biosynthe... -

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Basic information

Entry
Database: PDB / ID: 9bxl
TitleOvoM from Sulfuricurvum sp. isolate STB_99, an ovothiol-biosynthetic N-methyltransferase in complex with SAM
Components5-thiohistidine N-methyltransferase OvoM
KeywordsTRANSFERASE / ovothiol / S-adenosyl-L-methionine / 5-thiohistidine / 5-selenohistidine
Function / homologyS-ADENOSYLMETHIONINE
Function and homology information
Biological speciesSulfuricurvum sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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-thiohistidine N-methyltransferase OvoM
B: 5-thiohistidine N-methyltransferase OvoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9329
Polymers62,7042
Non-polymers1,2277
Water5,224290
1
B: 5-thiohistidine N-methyltransferase OvoM
hetero molecules

A: 5-thiohistidine N-methyltransferase OvoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9329
Polymers62,7042
Non-polymers1,2277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area3570 Å2
ΔGint7 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 92.215, 95.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 5-thiohistidine N-methyltransferase OvoM


Mass: 31352.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfuricurvum sp. (bacteria) / Strain: STB_99 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: Small plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M citric acid, pH 5, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.09→48.27 Å / Num. obs: 37433 / % possible obs: 99.56 % / Redundancy: 2 % / Biso Wilson estimate: 34.15 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05425 / Rpim(I) all: 0.05425 / Rrim(I) all: 0.07673 / Net I/σ(I): 9.49
Reflection shellResolution: 2.09→2.165 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5509 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 3567 / CC1/2: 0.644 / CC star: 0.885 / Rpim(I) all: 0.5509 / Rrim(I) all: 0.7791 / % possible all: 96.36

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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: 2.09→48.27 Å / SU ML: 0.2707 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 1863 4.98 %
Rwork0.1913 35542 -
obs0.1928 37405 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.08 Å2
Refinement stepCycle: LAST / Resolution: 2.09→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 82 290 4218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764028
X-RAY DIFFRACTIONf_angle_d1.0495457
X-RAY DIFFRACTIONf_chiral_restr0.0556591
X-RAY DIFFRACTIONf_plane_restr0.0215693
X-RAY DIFFRACTIONf_dihedral_angle_d15.25491436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.34561290.28292554X-RAY DIFFRACTION93.91
2.15-2.210.31631440.26062674X-RAY DIFFRACTION99.61
2.21-2.280.3381330.2622729X-RAY DIFFRACTION100
2.28-2.360.27931480.24112697X-RAY DIFFRACTION99.89
2.36-2.460.29551440.2422704X-RAY DIFFRACTION100
2.46-2.570.2961440.22382735X-RAY DIFFRACTION100
2.57-2.70.24311460.20452733X-RAY DIFFRACTION99.97
2.7-2.870.27081390.20622709X-RAY DIFFRACTION99.93
2.87-3.090.23971430.21412751X-RAY DIFFRACTION99.97
3.09-3.410.21641460.19272767X-RAY DIFFRACTION100
3.41-3.90.18231440.16562754X-RAY DIFFRACTION99.9
3.9-4.910.16531480.13792801X-RAY DIFFRACTION99.9
4.91-48.270.18161550.17512934X-RAY DIFFRACTION99.81

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