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Yorodumi- PDB-6qe5: Structure of E.coli RlmJ in complex with the natural cofactor pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qe5 | ||||||
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Title | Structure of E.coli RlmJ in complex with the natural cofactor product S-adenosyl-homocysteine (SAH) | ||||||
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 PCN033 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 | 6qe5.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qe5.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qe5_validation.pdf.gz | 925.7 KB | Display | wwPDB validaton report |
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Full document | 6qe5_full_validation.pdf.gz | 926.8 KB | Display | |
Data in XML | 6qe5_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 6qe5_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qe5 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qe5 | HTTPS FTP |
-Related structure data
Related structure data | 6qdxC 6qe0C 6qe6C 4blvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34161.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli PCN033 (bacteria) / Gene: yhiR, rlmJ, PPECC33_03818 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0G3KF30, UniProt: P37634*PLUS, 23S rRNA (adenine2030-N6)-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M KSCN, 30% (w/v) polyethylene glycol methyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→43.23 Å / Num. obs: 67854 / % possible obs: 97.11 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07581 / Net I/σ(I): 9.89 |
Reflection shell | Resolution: 1.61→1.67 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BLV Resolution: 1.61→43.228 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→43.228 Å
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Refine LS restraints |
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LS refinement shell |
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