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Yorodumi- PDB-1vbz: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vbz | ||||||
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Title | Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Ba2+ solution | ||||||
Components |
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Keywords | TRANSLATION/RNA / HDV / ribozyme / RNA / U1A / precursor / TRANSLATION-RNA COMPLEX | ||||||
Function / homology | Function and homology information U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ke, A. / Zhou, K. / Ding, F. / Cate, J.H.D. / Doudna, J.A. | ||||||
Citation | Journal: NATURE / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbz.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbz.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbz ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbz | HTTPS FTP |
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-Related structure data
Related structure data | 1sj3C 1sj4C 1sjfC 1vbxC 1vbyC 1vc0C 1vc5C 1vc6C C: citing same article (ref.) |
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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: 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.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P09012 | ||
#3: Chemical | #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: 3.3 Å3/Da / Density % sol: 62.43 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: BaCl2, 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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35.4 Å / Num. all: 10911 / Num. obs: 9569 / % possible obs: 87.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.8 / Biso Wilson estimate: 39.2 Å2 |
Reflection shell | Resolution: 2.8→2.98 Å / % possible all: 73.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→33.43 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 360345.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1075 Å2 / ksol: 0.313212 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→33.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Total num. of bins used: 6
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Xplor file |
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