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- PDB-6yxt: Crystal structure of the ADP-bound form of choline kinase from Pl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yxt | ||||||
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Title | Crystal structure of the ADP-bound form of choline kinase from Plasmodium falciparum | ||||||
![]() | Choline kinase | ||||||
![]() | TRANSFERASE / choline kinase / ADP / complex | ||||||
Function / homology | ![]() Synthesis of PE / Synthesis of PC / choline kinase / ethanolamine kinase activity / choline kinase activity / phosphatidylethanolamine biosynthetic process / phosphatidylcholine biosynthetic process / choline binding / phosphorylation / nucleotide binding ...Synthesis of PE / Synthesis of PC / choline kinase / ethanolamine kinase activity / choline kinase activity / phosphatidylethanolamine biosynthetic process / phosphatidylcholine biosynthetic process / choline binding / phosphorylation / nucleotide binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torretta, A. / Parisini, E. | ||||||
![]() | ![]() Title: Crystal Structure of the Apo and the ADP-Bound Form of Choline Kinase from Plasmodium falciparum Authors: Torretta, A. / Lopez-Cara, L.C. / Parisini, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yxsC ![]() 3fi8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45334.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PF3D7_1401800 / Production host: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.04 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% (v/v) PEG 4000, 0.2 M NaCl, 0.1 M HEPES pH 7.5, 2 mM TCEP, 4 mM MgCl2 and 2 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→68 Å / Num. obs: 24873 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3571 / CC1/2: 0.486 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FI8 Resolution: 2.2→56.17 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.81 Å2 / Biso mean: 57.1555 Å2 / Biso min: 26.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→56.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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