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Yorodumi- PDB-7q7x: Crystal structure of the methyltransferase-ribozyme 1 (with 1-met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q7x | ||||||
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Title | Crystal structure of the methyltransferase-ribozyme 1 (with 1-methyl-adenosine) | ||||||
Components |
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Keywords | RNA / MTR1 / methyltransferase ribozyme / ribozyme | ||||||
Function / homology | GUANINE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mieczkowski, M. / Hoebartner, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Structure and mechanism of the methyltransferase ribozyme MTR1. Authors: Scheitl, C.P.M. / Mieczkowski, M. / Schindelin, H. / Hobartner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q7x.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q7x.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 7q7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q7x_validation.pdf.gz | 412.5 KB | Display | wwPDB validaton report |
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Full document | 7q7x_full_validation.pdf.gz | 412.8 KB | Display | |
Data in XML | 7q7x_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 7q7x_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/7q7x ftp://data.pdbj.org/pub/pdb/validation_reports/q7/7q7x | HTTPS FTP |
-Related structure data
Related structure data | 7q7yC 7q7zC 7q80C 7q81C 7q82C 7oaxS 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
-RNA chain , 3 types, 3 molecules ABC
#1: RNA chain | Mass: 4436.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 7641.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 7755.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 18 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GUN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 36-42% MPD, 50mM MES pH 6.4-6.7, 100mM NaCl, 100mM LiCl, 10mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9198 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.94 Å / Num. obs: 5592 / % possible obs: 99.9 % / Redundancy: 24.8 % / Biso Wilson estimate: 97.24 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.74 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 25.5 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 533 / CC1/2: 0.664 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OAX Resolution: 2.8→42.94 Å / SU ML: 0.4034 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7579 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 104.42 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→42.94 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 44.9191011962 Å / Origin y: 12.9479958931 Å / Origin z: 41.9305967526 Å
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Refinement TLS group | Selection details: all |