+Open data
-Basic information
Entry | Database: PDB / ID: 1lik | |||||||||
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Title | STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE | |||||||||
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 / Resolution: 2.55 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 | 1lik.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lik.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1lik ftp://data.pdbj.org/pub/pdb/validation_reports/li/1lik | 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
#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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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | #5: 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: 46.24 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 27, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→10 Å / Num. obs: 30369 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.55→2.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.109 / % possible all: 75 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. obs: 17172 / % possible obs: 97 % / Num. measured all: 30369 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 81 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Resolution: 2.55→10 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.55→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / % reflection Rfree: 10 % / Rfactor obs: 0.13 / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.13 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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