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- PDB-6qe0: Structure of E.coli RlmJ in complex with a bisubstrate analogue (BA2) -

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Basic information

Entry
Database: PDB / ID: 6qe0
TitleStructure of E.coli RlmJ in complex with a bisubstrate analogue (BA2)
ComponentsRibosomal RNA large subunit methyltransferase J
KeywordsTRANSFERASE / RNA MTases / methyltransferase / m6A / transition state analogue / inhibitor / RNA binding / TrmK / RlmJ / m1A / structure.
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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HZ2 / Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.394 Å
AuthorsOerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
CitationJournal: Rna Biol. / Year: 2019
Title: Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Authors: Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
History
DepositionJan 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,9332
Polymers32,2721
Non-polymers6611
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.820, 58.400, 49.230
Angle α, β, γ (deg.)90.00, 97.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase J / 23STSA4 / rRNA (adenine(2030)-N6)-methyltransferase / 23S rRNA m6A2030 methyltransferase


Mass: 32271.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yhiR, rlmJ, PPECC33_03818 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0G3KF30, UniProt: P37634*PLUS, 23S rRNA (adenine2030-N6)-methyltransferase
#2: Chemical ChemComp-HZ2 / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[[9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethyl]amino]-2-azanyl-butanoic acid


Mass: 660.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36N12O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-Tris pH 6.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.39→37.46 Å / Num. obs: 53277 / % possible obs: 98.68 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.0759 / Net I/σ(I): 12.71
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 2.033

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLV

4blv


Resolution: 1.394→37.46 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.12
RfactorNum. reflection% reflection
Rfree0.2664 2642 4.99 %
Rwork0.2244 --
obs0.2265 52895 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.394→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 47 264 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062344
X-RAY DIFFRACTIONf_angle_d0.93181
X-RAY DIFFRACTIONf_dihedral_angle_d16.552889
X-RAY DIFFRACTIONf_chiral_restr0.075345
X-RAY DIFFRACTIONf_plane_restr0.005402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3944-1.41970.46021170.44642292X-RAY DIFFRACTION87
1.4197-1.4470.50671400.4522668X-RAY DIFFRACTION99
1.447-1.47660.45781370.43972592X-RAY DIFFRACTION99
1.4766-1.50870.45221400.4382658X-RAY DIFFRACTION99
1.5087-1.54380.47331400.42792661X-RAY DIFFRACTION99
1.5438-1.58240.44611410.39332634X-RAY DIFFRACTION98
1.5824-1.62520.43461380.38652609X-RAY DIFFRACTION99
1.6252-1.6730.42361360.37392625X-RAY DIFFRACTION99
1.673-1.7270.38311380.35512663X-RAY DIFFRACTION99
1.727-1.78870.44071410.35882657X-RAY DIFFRACTION100
1.7887-1.86040.33571400.32282654X-RAY DIFFRACTION100
1.8604-1.9450.32061410.27032685X-RAY DIFFRACTION100
1.945-2.04760.30621400.24942669X-RAY DIFFRACTION100
2.0476-2.17590.3031420.24572690X-RAY DIFFRACTION100
2.1759-2.34390.29671410.2432687X-RAY DIFFRACTION100
2.3439-2.57970.24971400.21592657X-RAY DIFFRACTION100
2.5797-2.9530.2451420.19452691X-RAY DIFFRACTION100
2.953-3.72020.22621430.16572713X-RAY DIFFRACTION100
3.7202-47.45770.16751450.15172748X-RAY DIFFRACTION100

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