+Open data
-Basic information
Entry | Database: PDB / ID: 8pry | ||||||
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Title | Crystal structure of Trypanosoma cruzi glycerol kinase | ||||||
Components | glycerol kinase | ||||||
Keywords | TRANSFERASE / Glycerol metabolism / Trypanosoma cruzi / Glycosomes. | ||||||
Function / homology | Function and homology information glycerol-3-phosphate biosynthetic process / glycerol kinase / glycerol kinase activity / glycerol catabolic process / triglyceride metabolic process / phosphorylation / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Lipinski, O. / Sonani, R.R. / Dubin, G. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Trypanosoma cruzi glycerol kinase in complex with glycerol Authors: Lipinski, O. / Sonani, R.R. / Dubin, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pry.cif.gz | 797.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pry.ent.gz | 662.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8pry ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8pry | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 58270.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_2g784 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2W444 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 20% w/v Polyethylene glycol 3350, 200 mM Magnesium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→44.61 Å / Num. obs: 117172 / % possible obs: 93.84 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.07→2.11 Å / Num. unique obs: 4908 / CC1/2: 0.518 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→44.61 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 17.018 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.196 / 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: 44.092 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→44.61 Å
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Refine LS restraints |
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