+Open data
-Basic information
Entry | Database: PDB / ID: 7bb3 | ||||||
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Title | Structure of S. pombe YG-box oligomer | ||||||
Components | Survival motor neuron-like protein 1,Survival motor neuron-like protein 1 | ||||||
Keywords | SPLICING / UsnRNP / Biogenesis / SMN / Oligomerization | ||||||
Function / homology | : / SMN complex / mRNA cis splicing, via spliceosome / spliceosomal snRNP assembly / RNA binding / nucleus / SMN complex subunit smn1 Function and homology information | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.158 Å | ||||||
Authors | Veepaschit, J. / Grimm, C. / Fischer, U. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Identification and structural analysis of the Schizosaccharomyces pombe SMN complex. Authors: Veepaschit, J. / Viswanathan, A. / Bordonne, R. / Grimm, C. / Fischer, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bb3.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bb3.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bb3 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bb3 | HTTPS FTP |
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-Related structure data
Related structure data | 7bblC 4rg5S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8162.006 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: smn1, yab8, SPAC2G11.08c / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09808 #2: Chemical | ChemComp-MPD / ( #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.61 Å3/Da / Density % sol: 65.9 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 65 % 2-methylpentanediol, 80 mM KCl, 40 mM HEPES / PH range: 6.8-7.2 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2016 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 2.158→40.493 Å / Num. obs: 10282 / % possible obs: 99.38 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.47 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1046 / Rpim(I) all: 0.04472 / Rrim(I) all: 0.1142 / Net I/σ(I): 10.85 |
Reflection shell | Resolution: 2.158→2.235 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1010 / CC1/2: 0.708 / CC star: 0.911 / Rpim(I) all: 0.3344 / Rrim(I) all: 0.8907 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RG5 Resolution: 2.158→40.493 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 37.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.82 Å2 / Biso min: 33.29 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.158→40.493 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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