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Yorodumi- PDB-1drz: U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1drz | ||||||
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Title | U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / CATALYTIC RNA / RIBOZYME / RNA-BINDING PROTEIN / U1A / HDV / RNA BINDING PROTEIN-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 | Hepatitis delta virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Ferre-D'Amare, A.R. / Zhou, K. / Doudna, J.A. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Crystal structure of a hepatitis delta virus ribozyme. Authors: Ferre-D'Amare, A.R. / Zhou, K. / 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 | 1drz.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1drz.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 1drz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/1drz ftp://data.pdbj.org/pub/pdb/validation_reports/dr/1drz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 23179.793 Da / Num. of mol.: 1 / Fragment: RIBOZYME DOMAIN Source method: isolated from a genetically manipulated source Details: RNA IS THE PRODUCT OF SELF-CLEAVAGE. NUCLEOTIDES 146 - 159 INCLUSIVE ARE AN ENGINEERED COGNATE BINDING SITE FOR THE U1A PROTEIN Source: (gene. exp.) Hepatitis delta virus / Genus: Deltavirus Description: RNA PRODUCED BY IN VITRO RUN-OFF TRANSCRIPTION WITH BACTERIOPHAGE T7 RNA POLYMERASE FROM PLASMID DNA LINEARIZED WITH RESTRICTION ENZYME BSAI. T7 TRANSCRIPT Plasmid: PDU9 / Production host: Escherichia coli (E. coli) | ||||
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#2: Protein | Mass: 11396.701 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN / Mutation: Y31H, Q36R Source method: isolated from a genetically manipulated source Details: SELENOMETHIONYL PROTEIN / Source: (gene. exp.) Homo sapiens (human) Description: (A1-98 Y31H Q36R) T7 PLASMID EXPRESSED IN E. COLI STRAIN B834 GROWN IN MINIMAL MEDIUM SUPPLEMENTED WITH SELENOMETHIONINE; Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P09012 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 67 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9761, 0.9794, 0.9792, 1.1390 | |||||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 1998 / Details: MIRROR | |||||||||||||||
Radiation | Monochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→41.3 Å / Num. all: 17817 / Num. obs: 17817 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.7 | |||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.2 / % possible all: 97.6 | |||||||||||||||
Reflection | *PLUS Num. measured all: 55889 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 2082995.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.3 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 76.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.399 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.426 |