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Yorodumi- PDB-1lii: STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE 2 AND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lii | |||||||||
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Title | STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE 2 AND AMP-PCP | |||||||||
Components | adenosine kinase | |||||||||
Keywords | TRANSFERASE / ALPHA-BETA STRUCTURE | |||||||||
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 / Resolution: 1.73 Å | |||||||||
Authors | Schumacher, M.A. / Scott, D.M. / Mathews, I.I. / Ealick, S.E. / Roos, D.S. / Ullman, B. / Brennan, R.G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding. Authors: Schumacher, M.A. / Scott, D.M. / Mathews, I.I. / Ealick, S.E. / Roos, D.S. / Ullman, B. / Brennan, R.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lii.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lii.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1lii ftp://data.pdbj.org/pub/pdb/validation_reports/li/1lii | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38373.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: PBACE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TVW2, adenosine kinase |
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-Non-polymers , 5 types, 174 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ADN / |
#5: Chemical | ChemComp-ACP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.23 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulphate, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→10 Å / Num. obs: 38408 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.72→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.242 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 1.71 Å / Lowest resolution: 10 Å / % possible obs: 99 % / Num. measured all: 132352 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Resolution: 1.73→10 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.73→10 Å
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.178 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.178 / Highest resolution: 1.71 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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