[English] 日本語
![](img/lk-miru.gif)
- PDB-2a9y: Crystal structure of T. gondii adenosine kinase complexed with N6... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2a9y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T. gondii adenosine kinase complexed with N6-dimethyladenosine | ||||||
![]() | adenosine kinase | ||||||
![]() | SIGNALING PROTEIN / TRANSFERASE / ribokinase fold / alpha/beta | ||||||
Function / homology | ![]() adenosine kinase / adenosine kinase activity / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / el Kouni, M.H. / Ealick, S.E. | ||||||
![]() | ![]() Title: Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase Authors: Zhang, Y. / El Kouni, M.H. / Ealick, S.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 174.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 135.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1007.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1013.5 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a9zC ![]() 2aa0C ![]() 2ab8C ![]() 1lioS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40584.105 Da / Num. of mol.: 1 / Mutation: G270S, S360F, L361T, P362S, C363G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 410 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/26A.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/26A.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.8 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, ammonium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2004 |
Radiation | Monochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 72440 / Num. obs: 72440 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.06 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 5480 / Rsym value: 0.378 / % possible all: 73.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1LIO Resolution: 1.35→10 Å / Num. parameters: 28776 / Num. restraintsaints: 36552 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.1%
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 30 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3046 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.42 Å /
|