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Yorodumi- PDB-2k2t: Epidermal growth Factor-like domain 2 from Toxoplasma gondii Micr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k2t | ||||||
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Title | Epidermal growth Factor-like domain 2 from Toxoplasma gondii Microneme protein 6 | ||||||
Components | Micronemal protein 6 | ||||||
Keywords | CELL ADHESION / EGF / MIC6 / Toxoplasma gondii / apicomplexa / protozoa / Cytoplasmic vesicle / EGF-like domain / Membrane / Transmembrane / Virulence | ||||||
Function / homology | Function and homology information microneme membrane / cytoplasmic vesicle / cell adhesion / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Sawmynaden, K. / Saouros, S. / Marchant, J. / Simpson, P. / Matthews, S. | ||||||
Citation | Journal: Embo Rep. / Year: 2008 Title: Structural insights into microneme protein assembly reveal a new mode of EGF domain recognition. Authors: Sawmynaden, K. / Saouros, S. / Friedrich, N. / Marchant, J. / Simpson, P. / Bleijlevens, B. / Blackman, M.J. / Soldati-Favre, D. / Matthews, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k2t.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k2t.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 2k2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/2k2t ftp://data.pdbj.org/pub/pdb/validation_reports/k2/2k2t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6366.056 Da / Num. of mol.: 1 / Fragment: EGF2-like domain 2 (UNP residues 87-147) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: MIC6 / Plasmid: pET32Xa/LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XYH7 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-98% 13C; U-98% 15N] Epidermal Growth Factor-like domain 2, 25 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | pH: 6.8 / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |