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Yorodumi- PDB-6wtl: Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wtl | |||||||||
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Title | Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold | |||||||||
Components | RNA (124-MER) | |||||||||
Keywords | RNA / microRNA / RNA processing | |||||||||
Function / homology | Chem-2BA / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Shoffner, G.M. / Peng, Z. / Guo, F. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography Authors: Shoffner, G.M. / Peng, Z. / Guo, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wtl.cif.gz | 151.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wtl.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wtl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6wtl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6wtl_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 6wtl_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wtl ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wtl | HTTPS FTP |
-Related structure data
Related structure data | 6n5kC 6n5nC 6n5oC 6n5pC 6n5qC 6n5sC 6n5tC 4qk8S 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
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 40249.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: in vitro transcription vector pT7-Fluc(deltai) (others) |
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-Non-polymers , 5 types, 9 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / | #5: Chemical | ChemComp-SO4 / | #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 grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 1.7 M (NH4)2SO4, 0.2 M LI2SO4, AND 0.1 M HEPES PH 7.1 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→75.491 Å / Num. obs: 21107 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 97.99 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 2.85→2.92 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1386 / CC1/2: 0.816 / Rpim(I) all: 0.358 / Rrim(I) all: 1.62 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QK8 Resolution: 2.85→75.491 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.54 / 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: 386.84 Å2 / Biso mean: 118.379 Å2 / Biso min: 47.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→75.491 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection Rfree: 10 %
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