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Yorodumi- PDB-5kb6: High-resolution structure of the adenosine kinase from Mus muscul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kb6 | ||||||
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Title | High-resolution structure of the adenosine kinase from Mus musculus in complex with adenosine | ||||||
Components | Adenosine kinase | ||||||
Keywords | TRANSFERASE / Adenosine Kinase | ||||||
Function / homology | Function and homology information dATP biosynthetic process / Purine salvage / Ribavirin ADME / adenosine kinase / adenosine kinase activity / dAMP salvage / deoxyadenosine kinase activity / adenosine metabolic process / GMP salvage / type B pancreatic cell proliferation ...dATP biosynthetic process / Purine salvage / Ribavirin ADME / adenosine kinase / adenosine kinase activity / dAMP salvage / deoxyadenosine kinase activity / adenosine metabolic process / GMP salvage / type B pancreatic cell proliferation / AMP salvage / purine ribonucleoside salvage / positive regulation of cardiac muscle hypertrophy / purine nucleobase metabolic process / positive regulation of T cell proliferation / phosphorylation / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å | ||||||
Authors | Oliveira, R.R. / Neto, R.M. / Polo, C.C. / Tonoli, C.C.C. / Murakami, M.T. / Franchini, K.G. | ||||||
Citation | Journal: To Be Published Title: High-resolution structure of the adenosine kinase from Mus musculus in complex with adenosine Authors: Oliveira, R.R. / Neto, R.M. / Polo, C.C. / Tonoli, C.C.C. / Murakami, M.T. / Franchini, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kb6.cif.gz | 557 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kb6.ent.gz | 456.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/5kb6 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kb6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40344.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adk / Production host: Escherichia coli (E. coli) / References: UniProt: P55264, adenosine kinase |
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-Non-polymers , 6 types, 492 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 50% (v/v) PEG400 0.2 M lithium sulphate 0.1 M sodium acetate 2.5 mM adenosine |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.954 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 228026 / % possible obs: 99.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 22.889 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.2→20.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.416 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.68 Å2 / Biso mean: 19.828 Å2 / Biso min: 8.47 Å2
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Refinement step | Cycle: final / Resolution: 1.2→20.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.199→1.23 Å / Total num. of bins used: 20
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