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- PDB-5azj: Crystal structure of glycerol kinase from Trypanosoma brucei gamb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5azj | ||||||
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Title | Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP (with disulfide bridge) | ||||||
![]() | (Glycerol kinase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tokuoka, S.M. / Tokumasu, F. / Sakamoto, K. / Michels, P.A.M. / Harada, S. / Kita, K. | ||||||
![]() | ![]() Title: Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity. Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tokuoka, S.M. / Tokumasu, F. / Sakamoto, K. / Kido, Y. / Michels, P.A.M. / Watanabe, Y.I. / Harada, S. / Kita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 781.8 KB | Display | ![]() |
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PDB format | ![]() | 653 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5aziC ![]() 3wxlS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 57064.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: gk / Plasmid: pET151 / Production host: ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 57144.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: gk / Plasmid: pET151 / Production host: ![]() ![]() ![]() ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-GOL / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 18, 2015 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→50 Å / Num. all: 70299 / Num. obs: 69743 / % possible obs: 99.2 % / Observed criterion σ(I): -1.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.53 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3WXL Resolution: 2.61→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 24.232 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / 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: 47.036 Å2
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Refinement step | Cycle: 1 / Resolution: 2.61→20 Å
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Refine LS restraints |
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