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Yorodumi- PDB-8dhu: Crystal structure of LARP-DM15 from Drosophila melanogaster bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dhu | |||||||||
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Title | Crystal structure of LARP-DM15 from Drosophila melanogaster bound to m7GpppC | |||||||||
Components | La-related protein 1 | |||||||||
Keywords | RNA BINDING PROTEIN / LARP / DM15 | |||||||||
Function / homology | Function and homology information extrinsic component of mitochondrial outer membrane / spindle assembly involved in male meiosis / syncytial blastoderm mitotic cell cycle / mitochondrion inheritance / positive regulation of mitochondrial DNA replication / poly-pyrimidine tract binding / RNA cap binding / male meiotic nuclear division / positive regulation of cytoplasmic translation / mRNA stabilization ...extrinsic component of mitochondrial outer membrane / spindle assembly involved in male meiosis / syncytial blastoderm mitotic cell cycle / mitochondrion inheritance / positive regulation of mitochondrial DNA replication / poly-pyrimidine tract binding / RNA cap binding / male meiotic nuclear division / positive regulation of cytoplasmic translation / mRNA stabilization / negative regulation of cytoplasmic translation / positive regulation of translation / mRNA 5'-UTR binding / cytoplasmic stress granule / RNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å | |||||||||
Authors | Nguyen, E. / Berman, A.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution Authors: Nguyen, E. / Berman, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dhu.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dhu.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 8dhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/8dhu ftp://data.pdbj.org/pub/pdb/validation_reports/dh/8dhu | HTTPS FTP |
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-Related structure data
Related structure data | 8dioC 5v87S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 18563.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: larp, CG42551 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VAW5 #2: Chemical | ChemComp-91P / [[( | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.05 M Bicine, pH 9, 2.5% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.295→44.01 Å / Num. obs: 17090 / % possible obs: 99.65 % / Redundancy: 2 % / Biso Wilson estimate: 49.52 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01978 / Rrim(I) all: 0.02797 / Net I/σ(I): 17.01 |
Reflection shell | Resolution: 2.295→2.377 Å / Rmerge(I) obs: 0.2632 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 1695 / CC1/2: 0.8 / Rrim(I) all: 0.3722 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V87 Resolution: 2.295→44.01 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.295→44.01 Å
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Refine LS restraints |
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LS refinement shell |
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