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Yorodumi- PDB-4gu2: Crystal structure of ubiquitin from Entamoeba histolytica to 1.35... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gu2 | ||||||
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Title | Crystal structure of ubiquitin from Entamoeba histolytica to 1.35 Angstrom | ||||||
Components | Ubiquitin | ||||||
Keywords | PROTEIN BINDING / ubiquitin / ubiquitin-like modifier / ubiquitin fold / post-translational ubiquitination / isopeptide bond / EhUbc5 / EhUba1 | ||||||
Function / homology | Function and homology information modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Bosch, D.E. / Siderovski, D.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica. Authors: Bosch, D.E. / Siderovski, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gu2.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gu2.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/4gu2 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4gu2 | HTTPS FTP |
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-Related structure data
Related structure data | 4gprC 4gswC 1ubqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8982.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) Gene: EhUBI1, EHI_083270, EHI_083410, EHI_156660, EHI_178340 Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / References: UniProt: C4M760 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: EhUbiquitin at 17 mg/mL was mixed 1:1 with and equilibrated against crystallization solution containing 25% (w/v) PEG 3350 and 100 mM citric acid, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→25.654 Å / Num. all: 20637 / Num. obs: 20493 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 100 |
Reflection shell | Resolution: 1.35→1.36 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 6.9 / Num. unique all: 486 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1UBQ Resolution: 1.35→25.65 Å / SU ML: 0.14 / σ(F): 1.38 / Phase error: 30.66 / 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: 1.35→25.65 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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