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- PDB-7p9o: Structure of E.coli RlmJ in complex with a SAM analogue (CA) -

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Basic information

Entry
Database: PDB / ID: 7p9o
TitleStructure of E.coli RlmJ in complex with a SAM analogue (CA)
ComponentsRibosomal RNA large subunit methyltransferase J
KeywordsRNA BINDING PROTEIN / RNA MTases / methyltransferase / SAM analogue / m6A / RNA binding / SAM conjugate / RlmJ / conjugate analogue / RNA recognition / bisubstrate analogue
Function / homology
Function and homology information


23S rRNA (adenine2030-N6)-methyltransferase / 23S rRNA (adenine(2030)-N(6))-methyltransferase activity / rRNA (adenine-N6-)-methyltransferase activity / carbon utilization / rRNA base methylation / RNA binding / cytosol
Similarity search - Function
Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase D, RlmJ / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-0Y0 / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.095 Å
AuthorsMeynier, V. / Catala, M. / Oerum, S. / Barraud, P. / Tisne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE07-0028 France
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.
Authors: Meynier, V. / Iannazzo, L. / Catala, M. / Oerum, S. / Braud, E. / Atdjian, C. / Barraud, P. / Fonvielle, M. / Tisne, C. / Etheve-Quelquejeu, M.
History
DepositionJul 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3572
Polymers31,9901
Non-polymers3671
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.990, 38.890, 90.650
Angle α, β, γ (deg.)90.000, 105.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase J / 23S rRNA (adenine(2030)-N6)-methyltransferase / 23S rRNA m6A2030 methyltransferase


Mass: 31989.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rlmJ, yhiR, b3499, JW3466 / Plasmid: pET15B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P37634, 23S rRNA (adenine2030-N6)-methyltransferase
#2: Chemical ChemComp-0Y0 / 5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine


Mass: 367.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5 28% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.095→43.651 Å / Num. obs: 15974 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Net I/σ(I): 12.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.442 / Num. unique obs: 1224 / CC1/2: 0.966 / Rpim(I) all: 0.184 / Rrim(I) all: 0.479 / % possible all: 92.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QDX

6qdx


Resolution: 2.095→43.651 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3056 799 5.01 %
Rwork0.24 15160 -
obs0.2434 15959 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.86 Å2 / Biso mean: 22.7084 Å2 / Biso min: 2.43 Å2
Refinement stepCycle: final / Resolution: 2.095→43.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 46 101 2351
Biso mean--31.68 23.05 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0953-2.22650.37761280.2935242996
2.2265-2.39840.35311320.28842505100
2.3984-2.63980.35631320.28432519100
2.6398-3.02170.35841340.29142546100
3.0217-3.80660.28591350.21232551100

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