+Open data
-Basic information
Entry | Database: PDB / ID: 4n08 | ||||||
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Title | Structure of Trypanosoma brucei brucei adenosine kinase (apo) | ||||||
Components | Adenosine kinase | ||||||
Keywords | TRANSFERASE / anion hole / adenosine kinase | ||||||
Function / homology | Function and homology information purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / nucleoplasm ...purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Timm, J. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Structures of adenosine kinase from Trypanosoma brucei brucei. Authors: Timm, J. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n08.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n08.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 4n08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/4n08 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n08 | 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: 38228.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.6.2360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q584S0, adenosine kinase |
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#2: 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: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.1 M Tris, pH 8.8, 60% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→57.36 Å / Num. obs: 11649 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.292 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.298 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.681 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→43.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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