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Yorodumi- PDB-3px1: Structure of Calcium Binding Protein-1 from Entamoeba histolytica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3px1 | ||||||
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Title | Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Strontium | ||||||
Components | Calcium-binding protein | ||||||
Keywords | METAL BINDING PROTEIN / EF hand motif / calcium binding and signalling / kinase / Cytosol and phagocytic cup | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kumar, S. / Kumar, S. / Ahmad, E. / Khan, R.H. / Gourinath, S. | ||||||
Citation | Journal: To be Published Title: Flexibility and plasticity of EF-hand motifs: Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Pb2+, Ba2+, and Sr2+. Authors: Kumar, S. / Kumar, S. / Ahmad, E. / Khan, R.H. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3px1.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3px1.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 3px1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3px1_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 3px1_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 3px1_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3px1_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/3px1 ftp://data.pdbj.org/pub/pdb/validation_reports/px/3px1 | 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 Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: hm-1:imss / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38505 #2: Chemical | ChemComp-SR / #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: 2.81 Å3/Da / Density % sol: 56.2 % / Mosaicity: 1.174 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: MPD, Sodium Acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2008 / Details: Monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si111 or White Beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→82.64 Å / Num. all: 11558 / Num. obs: 6442 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Χ2: 1.259 / Net I/σ(I): 17.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NXQ Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.948 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.61 Å2 / Biso mean: 80.4157 Å2 / Biso min: 49.15 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.997→3.075 Å / Total num. of bins used: 20
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