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- PDB-7p9i: Structure of E.coli RlmJ in complex with an RNA conjugate (GAA-SAM) -

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Basic information

Entry
Database: PDB / ID: 7p9i
TitleStructure of E.coli RlmJ in complex with an RNA conjugate (GAA-SAM)
Components
  • RNA conjugate (GAA-SAM)
  • Ribosomal 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-6D6 / RNA / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.594 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 1.0Jun 1, 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

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase J
B: Ribosomal RNA large subunit methyltransferase J
D: RNA conjugate (GAA-SAM)
E: RNA conjugate (GAA-SAM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5856
Polymers65,7374
Non-polymers8492
Water10,215567
1
A: Ribosomal RNA large subunit methyltransferase J
D: RNA conjugate (GAA-SAM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2933
Polymers32,8682
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal RNA large subunit methyltransferase J
E: RNA conjugate (GAA-SAM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2933
Polymers32,8682
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.480, 57.590, 79.440
Angle α, β, γ (deg.)90.000, 98.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31989.607 Da / Num. of mol.: 2 / Mutation: K60E
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: RNA chain RNA conjugate (GAA-SAM)


Mass: 878.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-6D6 / 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine


Mass: 424.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28N8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.21 Å3/Da / Density % sol: 44.38 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 20% w/v PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.59→46.46 Å / Num. obs: 74189 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 14.5 / Num. measured all: 507892 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.59-1.646.41.4183274750890.5340.5931.5411.392.3
7.13-46.466.20.025549788410.0110.02743.899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QDX

6qdx


Resolution: 1.594→42.148 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 3706 5 %
Rwork0.1879 70429 -
obs0.1897 74135 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.16 Å2 / Biso mean: 21.7219 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 1.594→42.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 304 567 5240
Biso mean--20 31.18 -
Num. residues----544
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5943-1.61530.4221200.3798228285
1.6153-1.63740.36491440.33812725100
1.6374-1.66080.35831420.32712711100
1.6608-1.68560.34141420.30422697100
1.6856-1.71190.35051410.282675100
1.7119-1.740.31761460.25572768100
1.74-1.770.28571440.23762731100
1.77-1.80220.28931410.22432690100
1.8022-1.83690.22241430.20272712100
1.8369-1.87430.22491420.1942693100
1.8743-1.91510.21461430.19272718100
1.9151-1.95970.23611430.18842723100
1.9597-2.00870.22051430.19512710100
2.0087-2.0630.26081430.19772712100
2.063-2.12370.23761430.20392728100
2.1237-2.19220.2261430.18742715100
2.1922-2.27060.21771430.17822713100
2.2706-2.36150.20711430.17662725100
2.3615-2.46890.20731440.19032726100
2.4689-2.59910.2371440.18512738100
2.5991-2.76190.21131440.18152741100
2.7619-2.97510.2181450.18092741100
2.9751-3.27440.19251440.17532736100
3.2744-3.74790.19711440.16182739100
3.7479-4.7210.17881460.14412775100

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