[English] 日本語
Yorodumi- PDB-2abs: Crystal structure of T. gondii adenosine kinase complexed with AMP-PCP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2abs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T. gondii adenosine kinase complexed with AMP-PCP | ||||||
Components | adenosine kinase | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / ribokinase fold / alpha/beta / intermediate conformation | ||||||
Function / homology | Function and homology information adenosine kinase / adenosine kinase activity / AMP salvage / purine ribonucleoside salvage / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Zhang, Y. / el Kouni, M.H. / Ealick, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Structure of Toxoplasma gondii adenosine kinase in complex with an ATP analog at 1.1 angstroms resolution. Authors: Zhang, Y. / El Kouni, M.H. / Ealick, S.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2abs.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2abs.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 2abs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/2abs ftp://data.pdbj.org/pub/pdb/validation_reports/ab/2abs | HTTPS FTP |
---|
-Related structure data
Related structure data | 1lioS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#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.) Toxoplasma gondii (eukaryote) / Gene: AK / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9TVW2, adenosine kinase |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-ACP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.2 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 4000, ammonium acetate, magnesium chloride, sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9777 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2004 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. all: 129879 / Num. obs: 129879 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.062 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 9849 / Rsym value: 0.274 / % possible all: 71.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LIO Resolution: 1.1→10 Å / Num. parameters: 30575 / Num. restraintsaints: 42820 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.025
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 76 / Occupancy sum hydrogen: 2258.7 / Occupancy sum non hydrogen: 2967.97 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.15 Å /
|