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Yorodumi- PDB-7p8q: Structure of E.coli RlmJ in complex with an RNA conjugate (GA-SAM) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p8q | ||||||
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Title | Structure of E.coli RlmJ in complex with an RNA conjugate (GA-SAM) | ||||||
Components |
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Keywords | RNA 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 | ||||||
Biological species | Escherichia coli K-12 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.289 Å | ||||||
Authors | Meynier, V. / Catala, M. / Oerum, S. / Barraud, P. / Tisne, C. | ||||||
Funding support | France, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p8q.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p8q.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 7p8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p8q_validation.pdf.gz | 753.6 KB | Display | wwPDB validaton report |
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Full document | 7p8q_full_validation.pdf.gz | 757.7 KB | Display | |
Data in XML | 7p8q_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7p8q_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/7p8q ftp://data.pdbj.org/pub/pdb/validation_reports/p8/7p8q | HTTPS FTP |
-Related structure data
Related structure data | 7p9iC 7p9oC 6qdxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31989.607 Da / Num. of mol.: 1 / Mutation: K60E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rlmJ, yhiR, b3499, JW3466 / Plasmid: pET15B / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P37634, 23S rRNA (adenine2030-N6)-methyltransferase |
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#2: RNA chain | Mass: 549.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-6D6 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.57 % / Description: Plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1M BIS-TRIS pH 6.5 0.2M NaCl 25% w/v PEG 3350 |
-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: 0.978 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 17, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.289→39.5 Å / Num. obs: 12282 / % possible obs: 98.8 % / Redundancy: 6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1765 / Rpim(I) all: 0.07894 / Rrim(I) all: 0.1943 / Net I/σ(I): 7.59 |
Reflection shell | Resolution: 2.289→2.37 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.7592 / Num. unique obs: 1108 / CC1/2: 0.809 / Rpim(I) all: 0.3245 / Rrim(I) all: 0.8272 / % possible all: 89.94 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QDX Resolution: 2.289→39.5 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.17 / Phase error: 36.85 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 203.51 Å2 / Biso mean: 60.8363 Å2 / Biso min: 27.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.289→39.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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