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Yorodumi- PDB-2xtb: Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xtb | ||||||
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Title | Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kinase Complexed with Activator | ||||||
Components | ADENOSINE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
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 RHODESIENSE (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kuettel, S. / Greenwald, J. / Kostrewa, D. / Ahmed, S. / Scapozza, L. / Perozzo, R. | ||||||
Citation | Journal: Plos Negl Trop Dis / Year: 2011 Title: Crystal Structures of T. B. Rhodesiense Adenosine Kinase Complexed with Inhibitor and Activator: Implications for Catalysis and Hyperactivation. Authors: Kuettel, S. / Greenwald, J. / Kostrewa, D. / Ahmed, S. / Scapozza, L. / Perozzo, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xtb.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xtb.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xtb ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xtb | 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: 38131.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI RHODESIENSE (eukaryote) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q584S0, adenosine kinase |
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#2: Chemical | ChemComp-KRM / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST TWO RESIDUES ARE RESULT OF THROMBIN CLEAVAGE OF AFFINITY TAG. THE ALA IN POSITION TWO IS ...THE FIRST TWO RESIDUES ARE RESULT OF THROMBIN CLEAVAGE OF AFFINITY TAG. THE ALA IN POSITION TWO IS A CLONING ARTIFACT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→58 Å / Num. obs: 9747 / % possible obs: 98 % / Observed criterion σ(I): -10 / Redundancy: 3.2 % / Biso Wilson estimate: 47.2 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→58.42 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.824 / SU B: 18.003 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / 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: 32.347 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→58.42 Å
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