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Yorodumi- PDB-7q82: Crystal structure of the methyltransferase-ribozyme 1, Thallium d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q82 | ||||||
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Title | Crystal structure of the methyltransferase-ribozyme 1, Thallium derivative (with 1-methyl-adenosine) | ||||||
Components |
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Keywords | RNA / MTR1 / methyltransferase ribozyme / ribozyme | ||||||
Function / homology | GUANINE / THALLIUM (I) ION / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 7q82.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q82.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 7q82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/7q82 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/7q82 | HTTPS FTP |
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-Related structure data
Related structure data | 7q7xSC 7q7yC 7q7zC 7q80C 7q81C 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, 12 molecules
#4: Chemical | ChemComp-TL / #5: Chemical | ChemComp-GUN / | #6: Chemical | ChemComp-MG / | |
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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: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 36-42% MPD, 50mM MES (pH 6.5), 10mM sodium acetate, 100mM lithium acetate, 10mM magnesium acetate, 25mM thallium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9751 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9751 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→43.59 Å / Num. obs: 5037 / % possible obs: 99.9 % / Redundancy: 24.9 % / Biso Wilson estimate: 118.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.01 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 26.7 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 487 / CC1/2: 0.366 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Q7X Resolution: 2.95→43.59 Å / SU ML: 0.3924 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.1485 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: 123.94 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→43.59 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: 46.0646783124 Å / Origin y: 13.5021787497 Å / Origin z: 42.8249597586 Å
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Refinement TLS group | Selection details: all |