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- PDB-3mja: Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mja | ||||||
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Title | Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate, structure #2 | ||||||
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![]() | RNA / RNA psuedoknot / anions / selenate | ||||||
Function / homology | SELENATE ION / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kieft, J.S. / Golden, B.L. / Costantino, D.A. / Chase, E. | ||||||
![]() | ![]() Title: Identification and characterization of anion binding sites in RNA. Authors: Kieft, J.S. / Chase, E. / Costantino, D.A. / Golden, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.8 KB | Display | ![]() |
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PDB format | ![]() | 23.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.2 KB | Display | ![]() |
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Full document | ![]() | 398.6 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mj3C ![]() 3mjbC ![]() 3b31S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 9326.556 Da / Num. of mol.: 1 / Fragment: Domain 3 RNA / Mutation: U6178A / Source method: obtained synthetically / Details: In vitro transcription |
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#2: RNA chain | Mass: 4416.675 Da / Num. of mol.: 1 / Fragment: Domain 3 RNA / Mutation: A6199G / Source method: obtained synthetically |
#3: Chemical | ChemComp-SE4 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 1.8 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH; moved to 2.4 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 ...Details: 1.8 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH; moved to 2.4 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH (all otherfor cryoprotections, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42 Å / Num. obs: 8365 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 3B31 Resolution: 2.8→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 35 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 100.92 Å2 / Biso mean: 47.745 Å2 / Biso min: 27.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Xplor file |
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