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- PDB-9muj: RlmR 23S rRNA methyltransferase from Thermus thermophilus in comp... -

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Basic information

Entry
Database: PDB / ID: 9muj
TitleRlmR 23S rRNA methyltransferase from Thermus thermophilus in complex with methylated rRNA (Um2552) and S-adenosyl-L-homocysteine (SAH)
Components
  • 23S rRNA methyltransferase
  • RNA (59-MER)
KeywordsTRANSFERASE/RNA / 23S rRNA methyltransferase / SPOUT Family / complex / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


RNA methyltransferase activity / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / RNA binding / cytoplasm
Similarity search - Function
RNA 2-O ribose methyltransferase, substrate binding / : / MRM3-like substrate binding domain / RNA 2'-O ribose methyltransferase substrate binding / : / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / S-ADENOSYLMETHIONINE / : / RNA / RNA (> 10) / 23S rRNA methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsTanouti, Y. / Roovers, M. / Droogmans, L. / Van Elder, D. / Kruys, V. / Labar, G.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)FNRS BAG 20210875 Belgium
Fonds de la Recherche Scientifique (FNRS)FNRS BAG 20191372 Belgium
CitationJournal: To Be Published
Title: RlmR 23S rRNA methyltransferase from Thermus thermophilus in complex with methylated rRNA (Um2552) and S-adenosyl-L-homocysteine (SAH)
Authors: Tanouti, Y. / Roovers, M. / Droogmans, L. / Van Elder, D. / Kruys, V. / Labar, G.
History
DepositionJan 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S rRNA methyltransferase
B: 23S rRNA methyltransferase
C: RNA (59-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3685
Polymers79,5853
Non-polymers7832
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-19 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.920, 117.110, 58.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-437-

HOH

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Components

#1: Protein 23S rRNA methyltransferase


Mass: 30239.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1712 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q72GY4, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (59-MER)


Mass: 19105.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 4.5 / Details: Na-Citrate 0.1M, pH4.5, PEG6000 10%, LiCl 1M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.006→47.311 Å / Num. obs: 52487 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.133 / Net I/σ(I): 11.92
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.01-2.062.46438230.3862.5581
2.06-2.111.9937070.4842.0681
2.11-2.181.55436500.61.6181
2.18-2.241.2735250.731.3211
2.24-2.321.0734230.8121.1111
2.32-2.40.83633200.880.8671
2.4-2.490.66632020.9210.6911
2.49-2.590.52430810.9440.5431
2.59-2.70.41129910.9630.4271
2.7-2.840.31528270.9780.3271
2.84-2.990.23527100.9880.2451
2.99-3.170.17125830.9920.1791
3.17-3.390.12424240.9960.1281
3.39-3.660.0922610.9980.0941
3.66-4.010.07420850.9990.0761
4.01-4.480.0619080.9990.0621
4.48-5.180.05416790.9990.0561
5.18-6.340.0614670.9990.0621
6.34-8.970.04611430.9990.0481
8.97-47.3110.0396780.9990.041

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Processing

Software
NameVersionClassification
PHENIX1.11_2563refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.006→47.311 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 2578 4.91 %
Rwork0.2057 --
obs0.2071 52480 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→47.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 733 53 422 5141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114861
X-RAY DIFFRACTIONf_angle_d1.5726747
X-RAY DIFFRACTIONf_dihedral_angle_d20.1691959
X-RAY DIFFRACTIONf_chiral_restr0.123798
X-RAY DIFFRACTIONf_plane_restr0.018762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.006-2.04410.37091390.33562700X-RAY DIFFRACTION100
2.0441-2.08580.39591470.31892765X-RAY DIFFRACTION100
2.0858-2.13120.28031430.29522704X-RAY DIFFRACTION100
2.1312-2.18080.32321490.2752722X-RAY DIFFRACTION100
2.1808-2.23530.27421380.25972756X-RAY DIFFRACTION100
2.2353-2.29570.31261220.25662763X-RAY DIFFRACTION100
2.2957-2.36330.28921530.23972716X-RAY DIFFRACTION100
2.3633-2.43960.24741530.23672743X-RAY DIFFRACTION100
2.4396-2.52680.25611530.21962742X-RAY DIFFRACTION100
2.5268-2.62790.28121280.22192774X-RAY DIFFRACTION100
2.6279-2.74750.28511280.22312772X-RAY DIFFRACTION100
2.7475-2.89230.25761550.21452754X-RAY DIFFRACTION100
2.8923-3.07350.25611250.20562791X-RAY DIFFRACTION100
3.0735-3.31080.23231470.20942765X-RAY DIFFRACTION100
3.3108-3.64380.2121740.18782781X-RAY DIFFRACTION100
3.6438-4.17080.19111450.17472816X-RAY DIFFRACTION100
4.1708-5.25370.20521250.16822858X-RAY DIFFRACTION100
5.2537-47.30.21941540.20692980X-RAY DIFFRACTION100

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