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Yorodumi- PDB-5kvj: Crystal structure of the 16-mer doublestranded RNA. Northeast Str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kvj | ||||||
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Title | Crystal structure of the 16-mer doublestranded RNA. Northeast Structural Genomics Consortium (NESG) target RNA1 | ||||||
Components |
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Keywords | RNA / double stranded RNA / dsRNA / Northeast Structural Genomics Consortium / NESG / PSI-Biology | ||||||
Function / homology | ARGININE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.261 Å | ||||||
Authors | Vorobiev, S.M. / Ma, L.-C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: Crystal structure of the 16-mer double stranded RNA. Authors: Vorobiev, S.M. / Ma, L.-C. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kvj.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kvj.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kvj_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 5kvj_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 5kvj_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 5kvj_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/5kvj ftp://data.pdbj.org/pub/pdb/validation_reports/kv/5kvj | HTTPS FTP |
-Related structure data
Related structure data | 3nd3S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 5033.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 5193.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-ARG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under paraffin oil / pH: 9 Details: 2.4 M Ammonium sulfate, 0.1 M BICINE, pH 9.0, dsRNA buffer: 0.025M NH4OAc, pH 5.5, 0.275 M NaCl, 0.005 M CaCl2, 0.001 M EDTA, 0.001 M TCEP, 0.025 M Arg, and 0.02% NaN3 PH range: 7.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 3824 / % possible obs: 93.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.5 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nd3 Resolution: 2.261→21.649 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.261→21.649 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2605→21.6505 Å
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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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