+Open data
-Basic information
Entry | Database: PDB / ID: 2qpo | ||||||
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Title | Thermotoga Maritima Thymidine Kinase in the apo form | ||||||
Components | Thymidine kinase | ||||||
Keywords | TRANSFERASE / Apo-form / ATP-binding / Cytoplasm / DNA synthesis / Kinase / Nucleotide-binding | ||||||
Function / homology | Function and homology information thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / zinc ion binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Segura-Pena, D. / Lichter, J. / Trani, M. / Konrad, M. / Lavie, A. / Lutz, S. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes. Authors: Segura-Pena, D. / Lichter, J. / Trani, M. / Konrad, M. / Lavie, A. / Lutz, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qpo.cif.gz | 130 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qpo.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/2qpo ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qpo | 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: 20684.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tdk / Plasmid details: plasmid / Plasmid: pET-14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9WYN2, thymidine kinase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350 + 0.2 M NaSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 26, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→28.61 Å / Num. all: 44232 / Num. obs: 43333 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18.606 Å2 / Rsym value: 0.065 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 2375 / Rsym value: 0.225 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.61 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.046 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.582 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2444 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→28.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.002 Å / Total num. of bins used: 20
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