+Open data
-Basic information
Entry | Database: PDB / ID: 7dpe | ||||||
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Title | RNA methyltransferase METTL4 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Methyltransferase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleic acid metabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / nucleic acid binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.751 Å | ||||||
Authors | Luo, Q. / Ma, J.B. | ||||||
Citation | Journal: To Be Published Title: Structure of RNA m6A methyltransferase METTL4 in complex with DNA at 2.75 Angstroms resolutioon Authors: Luo, Q. / Ma, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dpe.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dpe.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 7dpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/7dpe ftp://data.pdbj.org/pub/pdb/validation_reports/dp/7dpe | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5518.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) | ||||
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#2: Protein | Mass: 47955.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g19340, F18O14.6 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
#3: Chemical | ChemComp-SAH / | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium malonate pH5.0 and 12% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→30 Å / Num. obs: 14645 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Χ2: 0.492 / Net I/σ(I): 5 / Num. measured all: 81664 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.751→29.324 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 26.89 / 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: 216.66 Å2 / Biso mean: 95.1262 Å2 / Biso min: 29.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.751→29.324 Å
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Refinement TLS params. | Method: refined / Origin x: -2.775 Å / Origin y: 12.299 Å / Origin z: 83.38 Å
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Refinement TLS group |
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