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Yorodumi- PDB-5c1s: Crystal structure of the GDP-bound fast hydrolyzing mutant (V71A/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c1s | |||||||||
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Title | Crystal structure of the GDP-bound fast hydrolyzing mutant (V71A/K73Q) of EhRabX3 from Entamoeba histolytica | |||||||||
Components | Small GTPase EhRabX3 | |||||||||
Keywords | HYDROLASE / P-loop containing nucleotide triphosphate hydrolases fold / Tandem GTPase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Entamoeba histolytica (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | |||||||||
Authors | Srivastava, V.K. / Chandra, M. / Datta, S. | |||||||||
Funding support | India, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Crystal Structure Analysis of Wild Type and Fast Hydrolyzing Mutant of EhRabX3, a Tandem Ras Superfamily GTPase from Entamoeba histolytica. Authors: Srivastava, V.K. / Chandra, M. / Saito-Nakano, Y. / Nozaki, T. / Datta, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c1s.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c1s.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 5c1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/5c1s ftp://data.pdbj.org/pub/pdb/validation_reports/c1/5c1s | HTTPS FTP |
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-Related 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: 45754.727 Da / Num. of mol.: 2 / Mutation: V71A, K73Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EhRabX3 / Plasmid: pET-28a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NT25 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 mM Ammonium citrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→38.624 Å / Num. obs: 13133 / % possible obs: 97.5 % / Redundancy: 25.6 % / Net I/σ(I): 20 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.1→38.62 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.38 / Stereochemistry target values: TWIN_LSQ_F
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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: 3.1→38.62 Å
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Refine LS restraints |
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LS refinement shell |
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