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- PDB-8h0s: Crystal structure of MnmM from B. subtilis complexed with Gln-TTG... -

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Basic information

Entry
Database: PDB / ID: 8h0s
TitleCrystal structure of MnmM from B. subtilis complexed with Gln-TTG anti-codon stem loop and SAM (2.90 A)
Components
  • Putative rRNA methylase YtqB
  • RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3')
KeywordsTRANSFERASE/RNA / Methyltransferase / tRNA post-transcriptional modification / MnmC mnm5(s2)U / TRANSFERASE-RNA complex
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
Putative rRNA methylase / Putative rRNA methylase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / Putative rRNA methylase YtqB
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, J. / Lee, J. / Cho, G.
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
DepositionSep 30, 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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative rRNA methylase YtqB
B: Putative rRNA methylase YtqB
C: Putative rRNA methylase YtqB
D: Putative rRNA methylase YtqB
X: RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3')
Y: RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,36710
Polymers99,7736
Non-polymers1,5944
Water1,982110
1
A: Putative rRNA methylase YtqB
D: Putative rRNA methylase YtqB
X: RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6845
Polymers49,8873
Non-polymers7972
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-26 kcal/mol
Surface area17380 Å2
MethodPISA
2
B: Putative rRNA methylase YtqB
C: Putative rRNA methylase YtqB
Y: RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6845
Polymers49,8873
Non-polymers7972
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-26 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.180, 60.755, 94.059
Angle α, β, γ (deg.)90.97, 93.10, 101.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative rRNA methylase YtqB


Mass: 22253.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: ytqB, BSU30490 / Plasmid: pLATE51 / Details (production host): C-terminally 6xHis tagged / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O34614, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3')


Mass: 5380.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH5.6, 30% w/v Polyethylene glycol 4,000, 3% w/v Trimethylamine N-oxide dihydrate

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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: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→93.88 Å / Num. obs: 18875 / % possible obs: 91.2 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.102 / Rrim(I) all: 0.195 / Net I/σ(I): 6.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3264 / CC1/2: 0.768 / Rpim(I) all: 0.607 / Rrim(I) all: 1.169 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSJan 10, 2022data reduction
STARANISOdata scaling
MOLREP11.9.02phasing
MxDCdata collection
PDB_EXTRACT3.27data extraction
Coot0.9.8.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PON

4pon


Resolution: 2.9→93.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 35.59 / SU ML: 0.567 / Cross valid method: THROUGHOUT / ESU R Free: 0.516 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 901 4.8 %RANDOM
Rwork0.24076 ---
obs0.24281 17930 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.123 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å20.84 Å27.38 Å2
2---8.95 Å21.66 Å2
3---3.52 Å2
Refinement stepCycle: 1 / Resolution: 2.9→93.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 710 108 110 6351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126419
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165673
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.6748856
X-RAY DIFFRACTIONr_angle_other_deg0.4071.58113115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.615711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.287513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53810926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.2687.5812880
X-RAY DIFFRACTIONr_mcbond_other6.2657.5812880
X-RAY DIFFRACTIONr_mcangle_it10.15713.6053579
X-RAY DIFFRACTIONr_mcangle_other10.15613.6063580
X-RAY DIFFRACTIONr_scbond_it5.7637.7353539
X-RAY DIFFRACTIONr_scbond_other5.767.7353539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.35614.0895278
X-RAY DIFFRACTIONr_long_range_B_refined13.78977.617264
X-RAY DIFFRACTIONr_long_range_B_other13.78877.637264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 80 -
Rwork0.379 1362 -
obs--97.56 %

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