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Yorodumi- PDB-5f3o: Crystal structure of EhRNaseIII229 from Entamoeba histolytica com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f3o | ||||||
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Title | Crystal structure of EhRNaseIII229 from Entamoeba histolytica complexed with Mn2+ | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | RNA BINDING PROTEIN / RNaseIII / non canonical Dicer / RNA processing / 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: 2.05 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 | 5f3o.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f3o.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f3o_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 5f3o_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 5f3o_validation.xml.gz | 16 KB | Display | |
Data in CIF | 5f3o_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f3o ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f3o | 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: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.6M (NH4)2SO4, 0.01M MgCl2, 0.05M Tris-HCl pH 7.5 |
-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: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 25785 / % possible obs: 95.3 % / Redundancy: 5.5 % / Net I/σ(I): 16.4 |
-Processing
Software |
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Refinement | Resolution: 2.05→44.864 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.24 / 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: 2.05→44.864 Å
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Refine LS restraints |
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LS refinement shell |
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