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- PDB-1vby: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vby | ||||||
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Title | Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound | ||||||
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![]() | TRANSLATION/RNA / HDV / ![]() ![]() | ||||||
Function / homology | ![]() U1 snRNP binding / U1 snRNP / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ke, A. / Zhou, K. / Ding, F. / Cate, J.H.D. / Doudna, J.A. | ||||||
![]() | ![]() Title: A Conformational Switch controls hepatitis delta virus ribozyme catalysis Authors: Ke, A. / Zhou, K. / Ding, F. / Cate, J.H.D. / Doudna, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1sj3C ![]() 1sj4C ![]() 1sjfC ![]() 1vbxC ![]() 1vbzC ![]() 1vc0C ![]() 1vc5C ![]() 1vc6C C: citing same article ( |
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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: 24467.521 Da / Num. of mol.: 1 / Mutation: C75U / Source method: obtained synthetically Details: RNA occurs from Hapatitis Delta Virus pathogen, in vitro transcription with pUc19 | ||||
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#2: Protein | Mass: 11498.472 Da / Num. of mol.: 1 / Fragment: U1A_RBD(residues 1-100) / Mutation: Y31H/Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.57 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MnCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→42.26 Å / Num. all: 10937 / Num. obs: 10698 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.7 / Biso Wilson estimate: 149.5 Å2 |
Reflection shell | Resolution: 2.9→3.08 Å / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.4471 Å2 / ksol: 0.284785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→42.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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