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Yorodumi- PDB-6j9x: Crystal structure of Trypanosoma brucei gambiense glycerol kinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j9x | ||||||
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Title | Crystal structure of Trypanosoma brucei gambiense glycerol kinase phosphorylated at Thr12(pyrophosphatase reaction) | ||||||
Components | (Glycerol kinase) x 2 | ||||||
Keywords | TRANSFERASE / TRYPANOSOMA / GLYCEROL KINASE / SUGAR KINASE SUPERFAMILY / GLYCOSOME | ||||||
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: 2.7 Å | ||||||
Authors | Balogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, Y. / Ibrahim, B. / Bringaud, F. / de Koning, H. / McKerrow, J.H. / Watanabe, Y. ...Balogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, Y. / Ibrahim, B. / Bringaud, F. / de Koning, H. / McKerrow, J.H. / Watanabe, Y. / Nozaki, T. / Michels, P.A.M. / Harada, S. / Kita, K. / Shiba, T. | ||||||
Citation | Journal: To Be Published Title: Glycerol Kinase of African Human Trypanosomes Possesses a Pyrophosphatase Activity. Authors: Balogun, E.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j9x.cif.gz | 398.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j9x.ent.gz | 324.7 KB | Display | PDB format |
PDBx/mmJSON format | 6j9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9x ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9x | HTTPS FTP |
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-Related structure data
Related structure data | 6jaeC 6jafC 3wxlS 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: 57144.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote) Gene: gk / Plasmid: PET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3+PRARE2) / References: UniProt: D3KVM3, glycerol kinase #2: Protein | Mass: 57064.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote) Gene: gk / Plasmid: PET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3+PRARE2) / References: UniProt: D3KVM3, glycerol kinase #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: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 8-18% PEG 400, 0.1M HEPES, 11% 1,6-HEXANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2018 |
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: 2.7→50 Å / Num. obs: 61873 / % possible obs: 95.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.25 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 18869 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WXL Resolution: 2.7→19.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.999 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / 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: 95.123 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→19.89 Å
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Refine LS restraints |
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