[English] 日本語
Yorodumi- PDB-3bo4: A relaxed active site following exon ligation by a group I intron -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bo4 | ||||||
---|---|---|---|---|---|---|---|
Title | A relaxed active site following exon ligation by a group I intron | ||||||
Components |
| ||||||
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: 3.33 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bo4.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bo4.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3bo4 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3bo4 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-DNA/RNA hybrid , 2 types, 2 molecules CD
#2: DNA/RNA hybrid | Mass: 5094.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ligated exons / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA/RNA hybrid | Mass: 2828.786 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN Source: (synth.) synthetic construct (others) |
-RNA chain / Protein , 2 types, 2 molecules BA
#1: RNA chain | Mass: 64057.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#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 |
-Non-polymers , 3 types, 51 molecules
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-K / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.51 % | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / pH: 6.8 Details: MPD, Sodium Cacodylate, Magnesium Acetate, Potassium Acetate, Cobalt Hexamine, Potassium Vanadate, pH 6.80, vapor diffusion, hanging drop, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9795 |
Detector | Type: ADSC / Detector: CCD / Date: Jul 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 22836 / % possible obs: 99.7 % |
Reflection shell | Resolution: 3.3→3.42 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.33→36.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.945 / SU B: 38.372 / SU ML: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 153.68 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.33→36.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.33→3.42 Å
|