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- PDB-3b5s: Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b5s | ||||||
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Title | Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'-O-methyl Modification at the Active Site | ||||||
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![]() | RNA / hairpin ribozyme / 2 / 6 diaminopurine / 2'-O-methyl | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | MacElrevey, C. / Krucinska, J. / Wedekind, J.E. | ||||||
![]() | ![]() Title: Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. Authors: MacElrevey, C. / Salter, J.D. / Krucinska, J. / Wedekind, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.5 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.5 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b58C ![]() 3b5aC ![]() 3b5fC ![]() 3b91C ![]() 3bbiC ![]() 3bbkC ![]() 3bbmC ![]() 3cr1C ![]() 2oueS 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
-RNA chain , 3 types, 3 molecules ABC
#1: RNA chain | Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid-phase synthesis at Keck Institute, Yale / References: ![]() |
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#2: RNA chain | Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: solid phase chemical synthesis at Dharmacon, Colorado References: ![]() |
#3: RNA chain | Mass: 6006.583 Da / Num. of mol.: 1 / Mutation: A38(N6G), U39C / Source method: obtained synthetically Details: solid phase chemical synthesis at Dharmacon, Colorado References: ![]() |
-Non-polymers , 3 types, 36 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 78 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2006 Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING |
Radiation | Monochromator: horizontal focusing 5.05 degree asymmetric cut Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40.49 Å / Num. all: 16976 / Num. obs: 16724 / % possible obs: 98.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 113.4 Å2 / Rsym value: 0.037 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1615 / Rsym value: 0.476 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OUE Resolution: 2.25→40.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 860219.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber / Details: Alternate conformation at U1 of chain A
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→40.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.48 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 4
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Xplor file |
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