[English] 日本語
Yorodumi- PDB-2a9z: Crystal structure of T. gondii adenosine kinase complexed with N6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a9z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T. gondii adenosine kinase complexed with N6-dimethyladenosine and 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 / purine nucleobase metabolic process / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Zhang, Y. / el Kouni, M.H. / Ealick, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a9z.cif.gz | 172.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a9z.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 2a9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a9z_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a9z_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2a9z_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 2a9z_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/2a9z ftp://data.pdbj.org/pub/pdb/validation_reports/a9/2a9z | HTTPS FTP |
-Related structure data
Related structure data | 2a9yC 2aa0C 2ab8C 1lioS S: Starting model for refinement C: citing same article (ref.) |
---|---|
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.) 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 |
---|
-Non-polymers , 5 types, 388 molecules
#2: Chemical | ChemComp-CL / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACP / | #6: 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: 41.8 % |
---|---|
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: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å |
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: 74024 / Num. obs: 74024 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.044 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 6405 / Rsym value: 0.303 / % possible all: 86 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LIO Resolution: 1.35→10 Å / Num. parameters: 28048 / Num. restraintsaints: 34952 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.063
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 15 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3033 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.41 Å /
|