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Yorodumi- PDB-6xjy: Crystal structure of a self-alkylating ribozyme - short time incu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xjy | |||||||||
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Title | Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate | |||||||||
Components |
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Keywords | RNA/IMMUNE SYSTEM / Self-alkylating ribozyme / Antibody-assisted RNA crystallography / RNA catalysis / RNA-Immune System complex | |||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) Aeropyrum pernix (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.156 Å | |||||||||
Authors | Koirala, D. / Piccirilli, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Structural basis for substrate binding and catalysis by a self-alkylating ribozyme. Authors: Krochmal, D. / Shao, Y. / Li, N.S. / DasGupta, S. / Shelke, S.A. / Koirala, D. / Piccirilli, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xjy.cif.gz | 250.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xjy.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/6xjy ftp://data.pdbj.org/pub/pdb/validation_reports/xj/6xjy | HTTPS FTP |
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-Related structure data
Related structure data | 6xjqC 6xjwC 6xjzC 6mwnS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: RNA chain | Mass: 18674.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Aeropyrum pernix (archaea) #2: Antibody | Mass: 27588.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 26351.588 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M ammonium fluoride, 10% PEG3350, pH 6.2 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2018 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.156→79.38 Å / Num. obs: 69519 / % possible obs: 97.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 44.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.072 / Rrim(I) all: 0.153 / Net I/av σ(I): 7.1 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.16→2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 1.867 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4237 / CC1/2: 0.295 / Rpim(I) all: 1.046 / Rrim(I) all: 2.148 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MWN Resolution: 2.156→61.851 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.36 / 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: 120.71 Å2 / Biso mean: 47.6681 Å2 / Biso min: 26.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.156→61.851 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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