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Yorodumi- PDB-5f3p: Crystal structure of a noncanonical Dicer protein from Entamoeba ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f3p | ||||||
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Title | Crystal structure of a noncanonical Dicer protein from Entamoeba histolytica | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | RNA BINDING PROTEIN / RNaseIII / non canonical Dicer / RNA procesing / Entamoeba histolytica | ||||||
Function / homology | ribonuclease III activity / Ribonuclease III, endonuclease domain superfamily / RNA processing / metal ion binding / Uncharacterized protein Function and homology information | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.904 Å | ||||||
Authors | Yu, X. / Gan, J.H. / Ma, J.B. | ||||||
Citation | Journal: To Be Published Title: Structural and functional study of a noncanonical Dicer protein in Entamoeba histolytica Authors: Yu, X. / Gan, J.H. / Ma, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f3p.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f3p.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f3p_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 5f3p_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 5f3p_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 5f3p_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f3p ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f3p | 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
#1: Protein | Mass: 22893.994 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_068740 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LU64 #2: Chemical | #3: 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: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 1.6 M (NH4)2SO4, 0.01 M MgCl2, 0.05 M Tris-HCl pH 7.5 PH range: 7.4-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 31630 / % possible obs: 94.8 % / Redundancy: 6.6 % / Net I/σ(I): 26.8 |
-Processing
Software |
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Refinement | Resolution: 1.904→28.73 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.73 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.904→28.73 Å
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Refine LS restraints |
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LS refinement shell |
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