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Yorodumi- PDB-6qe0: Structure of E.coli RlmJ in complex with a bisubstrate analogue (BA2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qe0 | ||||||
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Title | Structure of E.coli RlmJ in complex with a bisubstrate analogue (BA2) | ||||||
Components | Ribosomal RNA large subunit methyltransferase J | ||||||
Keywords | TRANSFERASE / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.394 Å | ||||||
Authors | Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qe0.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qe0.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qe0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qe0 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qe0 | HTTPS FTP |
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-Related structure data
Related structure data | 6qdxC 6qe5C 6qe6C 4blvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-HZ2 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-Tris pH 6.5, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.39→1.44 Å / Rmerge(I) obs: 2.033 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.394→37.46 Å
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Refine LS restraints |
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LS refinement shell |
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