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Yorodumi- PDB-5gn6: Crystal structure of glycerol kinase from Trypanosoma brucei gamb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gn6 | ||||||
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Title | Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17b | ||||||
Components | Glycerol kinase | ||||||
Keywords | TRANSFERASE / Glycerol kinase / inhibitor / drug / African trypanosomes | ||||||
Function / homology | Function and homology information glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol catabolic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei gambiense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. ...Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Faseb J. / Year: 2019 Title: Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase ofTrypanosoma brucei brucei. Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. ...Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y.I. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gn6.cif.gz | 399 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gn6.ent.gz | 326.2 KB | Display | PDB format |
PDBx/mmJSON format | 5gn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/5gn6 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/5gn6 | HTTPS FTP |
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-Related structure data
Related structure data | 5gn5C 5gn7C 5gn9C 3wxiS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 56606.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote) Gene: gk / Production host: Escherichia coli (E. coli) / References: UniProt: D3KVM3, glycerol kinase #2: Chemical | ChemComp-6Y0 / #3: Chemical | ChemComp-GOL / #4: 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: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL PH range: 7.2-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 14, 2014 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 80045 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.31 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WXI Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 10.333 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.803 / ESU R Free: 0.324 / 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: 41.897 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→20 Å
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Refine LS restraints |
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