[English] 日本語
Yorodumi- PDB-3ulg: Crystal structure of Calcium-Binding Protein-1 from Entamoeba his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ulg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Calcium-Binding Protein-1 from Entamoeba histolytica in complex with barium | ||||||
Components | Calcium-binding protein | ||||||
Keywords | METAL BINDING PROTEIN / Calcium-binding motif | ||||||
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: 3.2 Å | ||||||
Authors | Kumar, S. / Gourinath, S. | ||||||
Citation | Journal: BMC Biophys / Year: 2012 Title: Flexibility of EF-hand motifs: Structural and thermodynamic studies of Calcium Binding Protein- 1 from Entamoeba histolytica with Pb2+, Ba2+, and Sr2+ Authors: Kumar, S. / Ahmed, E. / Kumar, S. / Khan, R.H. / Gourinath, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ulg.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ulg.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ulg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ulg_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ulg_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 3ulg_validation.xml.gz | 7 KB | Display | |
Data in CIF | 3ulg_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulg ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulg | HTTPS FTP |
-Related structure data
Related structure data | 2nxqS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 / Gene: CaBP1 / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P38505 #2: Chemical | ChemComp-BA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 60-65% MPD, 0.05M Sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2009 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 5485 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 103.6 Å2 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NXQ Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.872 / SU B: 24.317 / SU ML: 0.408 / Cross valid method: THROUGHOUT / σ(F): 1.8 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 122.089 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.31 Å / Total num. of bins used: 20 /
|