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- PDB-5dqk: Two divalent metal ions and conformational changes play roles in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dqk | ||||||
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Title | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mg2+ | ||||||
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![]() | RNA / ribozyme / hammerhead | ||||||
Function / homology | : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mir, A. / Chen, J. / Neau, D. / Golden, B.L. | ||||||
![]() | ![]() Title: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction. Authors: Mir, A. / Chen, J. / Robinson, K. / Lendy, E. / Goodman, J. / Neau, D. / 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 | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.6 KB | Display | ![]() |
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Full document | ![]() | 403.2 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dh6C ![]() 5dh7C ![]() 5dh8C ![]() 5di2C ![]() 5di4C ![]() 3zd5S 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 on special symmetry positions |
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Components
#1: RNA chain | Mass: 15500.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA was made by in vitro transcription / Source: (synth.) synthetic construct (others) | ||
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#2: DNA/RNA hybrid | Mass: 6437.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized oligonucleotide / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 33% MPD, 0.4 M potassium chloride, 50 mM potassium acetate pH 5.0, 10 mM MgCl2 and 0.5mM spermine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→42 Å / Num. all: 9951 / Num. obs: 9951 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZD5 Resolution: 2.707→26.069 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 29.17 / 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: 2.707→26.069 Å
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Refine LS restraints |
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LS refinement shell |
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