+Open data
-Basic information
Entry | Database: PDB / ID: 5vy1 | ||||||
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Title | Crystal structure of the extended Tudor domain from BmPAPI | ||||||
Components | Tudor and KH domain-containing protein homolog | ||||||
Keywords | RNA BINDING PROTEIN / BmPAPI / Tudor / sDMA | ||||||
Function / homology | Function and homology information piRNA processing / spermatogenesis / mitochondrial outer membrane / cell differentiation / RNA binding Similarity search - Function | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Hubbard, P.A. / Pan, X. / McNally, R. / Ohtaki, A. / Honda, S. / Kirino, Y. / Murali, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural studies of the Tudor domain from the Bombyx homolog of Drosophila PAPI: Implication to piRNA biogenesis Authors: Hubbard, P.A. / Pan, X. / McNally, R. / Ohtaki, A. / Honda, S. / Kirino, Y. / Murali, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vy1.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vy1.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vy1 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vy1 | HTTPS FTP |
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-Related structure data
Related structure data | 5vqgSC 5vqhC 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: 26953.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: PAPI / Production host: Escherichia coli (E. coli) / References: UniProt: H9JD76 |
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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: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.95 M ammonium sulfate, 50 mM sodium acetate, pH 5.5 and 5% glucose. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→19.5 Å / Num. obs: 8655 / % possible obs: 87.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.05→3.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1274 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VQG Resolution: 3.05→19.064 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→19.064 Å
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Refine LS restraints |
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LS refinement shell |
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