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Open data
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Basic information
Entry | Database: PDB / ID: 6a8a | ||||||
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Title | Ribokinase from Leishmania donovani with ATP | ||||||
![]() | Ribokinase | ||||||
![]() | TRANSFERASE / Nucleotide binding / ATP binding / Metal ion binding / Ribokinase activity / Carbohydrate metabolic process / cytoplasm | ||||||
Function / homology | ![]() ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gatreddi, S. / Qureshi, I.A. | ||||||
![]() | ![]() Title: Unraveling structural insights of ribokinase from Leishmania donovani. Authors: Gatreddi, S. / Pillalamarri, V. / Vasudevan, D. / Addlagatta, A. / Qureshi, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.5 KB | Display | ![]() |
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PDB format | ![]() | 112.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zwyC ![]() 6a8bC ![]() 6a8cC ![]() 2fv7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37582.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: LDBPK_270430 / Plasmid: pET28a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 261 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 0.1M Citric acid, 3.4M Sodium chloride, 10mM Magnesium chloride, 10% Glycerol PH range: 3.5-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.41 Å / Num. obs: 65706 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.824 / Num. unique obs: 23365 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FV7 Resolution: 1.8→46.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.68 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.11 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.124 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→46.41 Å
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Refine LS restraints |
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