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Yorodumi- PDB-6xjw: Crystal structure of a self-alkylating ribozyme - alkylated form ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xjw | |||||||||
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Title | Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety | |||||||||
Components |
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Keywords | RNA/IMMUNE SYSTEM / Self-alkylating ribozyme / Antibody-assisted RNA crystallography / RNA catalysis / RNA-Immune System complex | |||||||||
Function / homology | 2-{[(4R)-4-hydroxyhexyl]oxy}ethyl pentanoate / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) Aeropyrum pernix (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.918 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 | 6xjw.cif.gz | 510.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xjw.ent.gz | 412.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xjw_validation.pdf.gz | 860.4 KB | Display | wwPDB validaton report |
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Full document | 6xjw_full_validation.pdf.gz | 873 KB | Display | |
Data in XML | 6xjw_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 6xjw_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/6xjw ftp://data.pdbj.org/pub/pdb/validation_reports/xj/6xjw | HTTPS FTP |
-Related structure data
Related structure data | 6xjqC 6xjyC 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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1 |
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2 |
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Unit cell |
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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: 24225.047 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: 23712.367 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: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | 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: 2.82 Å3/Da / Density % sol: 56.32 % |
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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: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.918→99.64 Å / Num. obs: 111123 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.054 / Rrim(I) all: 0.101 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.901 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5188 / CC1/2: 0.247 / Rpim(I) all: 1.175 / Rrim(I) all: 2.239 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MWN Resolution: 1.918→89.85 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.72 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.918→89.85 Å
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Refine LS restraints |
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LS refinement shell |
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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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