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Yorodumi- PDB-7did: Mycoplasma genitalium RNase R in complex with ribose methylated s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7did | ||||||
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Title | Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA | ||||||
Components |
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Keywords | HYDROLASE/RNA / RNA hydrolase / 2'-O-methylation sensitive / HYDROLASE / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information exoribonuclease II / exoribonuclease II activity / miRNA catabolic process / mRNA catabolic process / P-body / 3'-5'-RNA exonuclease activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Mycoplasma genitalium G37 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Abula, A. / Quan, X. / Li, X. / Yang, T. / Li, T. / Chen, Q. / Ji, X. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation. Authors: Abula, A. / Li, X. / Quan, X. / Yang, T. / Liu, Y. / Guo, H. / Li, T. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7did.cif.gz | 295.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7did.ent.gz | 232.6 KB | Display | PDB format |
PDBx/mmJSON format | 7did.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7did_validation.pdf.gz | 894.2 KB | Display | wwPDB validaton report |
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Full document | 7did_full_validation.pdf.gz | 897.4 KB | Display | |
Data in XML | 7did_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 7did_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/7did ftp://data.pdbj.org/pub/pdb/validation_reports/di/7did | HTTPS FTP |
-Related structure data
Related structure data | 7dcyC 7dicC 7dolC 5xguS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 85595.555 Da / Num. of mol.: 1 / Mutation: D284A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: G-37 / Gene: rnr, vacB, MG104 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P47350, exoribonuclease II |
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#2: RNA chain | Mass: 1285.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycoplasma genitalium G37 (bacteria) |
#3: Chemical | ChemComp-MG / |
#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: 2.83 Å3/Da / Density % sol: 56.52 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 100 mM KCl, 100 mM HEPES (pH 6.8), 15% PEG 5000MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 78483 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3891 / Rrim(I) all: 2.936 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XGU Resolution: 1.9→29.979 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / 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: 116.49 Å2 / Biso mean: 46.0262 Å2 / Biso min: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→29.979 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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