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Yorodumi- PDB-3bo3: A relaxed active site following exon ligation by a group I intron -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bo3 | ||||||
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Title | A relaxed active site following exon ligation by a group I intron | ||||||
Components |
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Keywords | NUCLEAR PROTEIN/RNA / group I intron / azoarcus / ribozyme / ligation / Acetylation / mRNA processing / mRNA splicing / Nucleus / Ribonucleoprotein / RNA-binding / Spliceosome / NUCLEAR 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å | ||||||
Authors | Lipchock, S.V. / Strobel, S.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: A relaxed active site after exon ligation by the group I intron Authors: Lipchock, S.V. / Strobel, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bo3.cif.gz | 157.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bo3.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bo3_validation.pdf.gz | 472.9 KB | Display | wwPDB validaton report |
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Full document | 3bo3_full_validation.pdf.gz | 485.9 KB | Display | |
Data in XML | 3bo3_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 3bo3_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3bo3 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3bo3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 3 types, 3 molecules BCD
#1: RNA chain | Mass: 64057.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 5110.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3' exon / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 2830.759 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN, 5' exon Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 11038.911 Da / Num. of mol.: 1 / Fragment: RRM 1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09012 |
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-Non-polymers , 3 types, 39 molecules
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-K / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.93 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 6.8 Details: MPD, Sodium Cacodylate, Magnesium Acetate, Potassium Acetate, Cobalt Hexamine, pH 6.80, vapor diffusion, hanging drop, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 21147 / % possible obs: 99.6 % |
Reflection shell | Resolution: 3.4→3.52 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 3.4→47.73 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.917 / SU B: 39.375 / SU ML: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 158.92 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→47.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.48 Å
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