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- PDB-8h1a: Crystal structure of MnmM from S. aureus in apo state (1.44 A) -

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Basic information

Entry
Database: PDB / ID: 8h1a
TitleCrystal structure of MnmM from S. aureus in apo state (1.44 A)
ComponentsrRNA methylase YtqB
KeywordsTRANSFERASE / Methyltransferase / tRNA post-transcriptional modification / MnmC mnm5(s2)U
Function / homologytRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / Putative rRNA methylase / Putative rRNA methylase / tRNA processing / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / tRNA (mnm(5)s(2)U34)-methyltransferase
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKim, J. / Cho, G. / Lee, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification.
Authors: Cho, G. / Lee, J. / Kim, J.
History
DepositionOct 1, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rRNA methylase YtqB
B: rRNA methylase YtqB


Theoretical massNumber of molelcules
Total (without water)43,9302
Polymers43,9302
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-13 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.494, 63.910, 135.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein rRNA methylase YtqB


Mass: 21964.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FXG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97965 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 1.44→47.34 Å / Num. obs: 67371 / % possible obs: 95.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 17.1
Reflection shellResolution: 1.44→1.54 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.955 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3369 / CC1/2: 0.605 / Rpim(I) all: 0.525 / Rrim(I) all: 2.025 / % possible all: 66.5

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Processing

Software
NameVersionClassification
MxDCdata collection
STARANISOdata scaling
XDSJan 10, 2022data reduction
MOLREP11.9.02phasing
Coot0.9.8.3model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model (UniProt: Q2FXG9)

Resolution: 1.44→47.34 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.075 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19218 3409 5.1 %RANDOM
Rwork0.15185 ---
obs0.15394 63959 84.1 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.467 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å2-0 Å2
2---0.29 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.44→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 0 307 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0182995
X-RAY DIFFRACTIONr_bond_other_d0.0020.022824
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.8594066
X-RAY DIFFRACTIONr_angle_other_deg1.2352.8216522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63624.967153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.031156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02647
X-RAY DIFFRACTIONr_mcbond_it2.0942.3511480
X-RAY DIFFRACTIONr_mcbond_other2.0842.3461478
X-RAY DIFFRACTIONr_mcangle_it2.8353.5211857
X-RAY DIFFRACTIONr_mcangle_other2.8263.5211857
X-RAY DIFFRACTIONr_scbond_it2.6792.811515
X-RAY DIFFRACTIONr_scbond_other2.6782.8121516
X-RAY DIFFRACTIONr_scangle_other3.3224.0652210
X-RAY DIFFRACTIONr_long_range_B_refined4.41130.1793288
X-RAY DIFFRACTIONr_long_range_B_other4.02129.4183203
X-RAY DIFFRACTIONr_rigid_bond_restr2.43235819
LS refinement shellResolution: 1.44→1.476 Å
RfactorNum. reflection% reflection
Rfree0.17 14 -
Rwork0.217 426 -
obs--7.54 %

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