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Yorodumi- PDB-3qjk: Structure of Calcium Binding Protein-1 from Entamoeba histolytica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qjk | ||||||
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Title | Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Lead | ||||||
Components | Calcium-binding protein | ||||||
Keywords | METAL BINDING PROTEIN / EF-hand | ||||||
Function / homology | Function and homology information regulation of actin filament bundle assembly / positive regulation of macropinocytosis / regulation of protein kinase activity / pseudopodium / phagocytic cup / actin monomer binding / phagocytosis / positive regulation of phagocytosis / actin filament binding / calcium ion binding ...regulation of actin filament bundle assembly / positive regulation of macropinocytosis / regulation of protein kinase activity / pseudopodium / phagocytic cup / actin monomer binding / phagocytosis / positive regulation of phagocytosis / actin filament binding / calcium ion binding / endoplasmic reticulum / cytoplasm Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.001 Å | ||||||
Authors | Kumar, S. / Gourinath, S. | ||||||
Citation | Journal: To be Published Title: Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Lead Authors: Kumar, S. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qjk.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qjk.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qjk_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 3qjk_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 3qjk_validation.xml.gz | 7 KB | Display | |
Data in CIF | 3qjk_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjk ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjk | HTTPS FTP |
-Related structure data
Related structure data | 2nxqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14970.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: cytosol / Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: EhCaBP1 / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P38505 #2: Chemical | ChemComp-PB / #3: Chemical | #4: 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: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 60-65% MPD, 50mM NaOAc, 5mM Pb(NO3)2, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 6777 / Num. obs: 6763 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.054 / Rsym value: 0.0364 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.054 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.364 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NXQ Resolution: 3.001→28.082 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / Isotropic thermal model: RESTRAINED / σ(F): 1.39 / Phase error: 29.01 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.955 Å2 / ksol: 0.312 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.1336 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.001→28.082 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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