+Open data
-Basic information
Entry | Database: PDB / ID: 6ksr | ||||||
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Title | Crystal structure of Hexokinase from Eimeria tenella | ||||||
Components | Phosphotransferase | ||||||
Keywords | TRANSFERASE / Hexokinase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information hexokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / D-glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding Similarity search - Function | ||||||
Biological species | Eimeria tenella (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Yuan, H. / Sun, M.F. / Wang, Y.H. / Liao, S.Q. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Hexokinase from Eimeria tenella Authors: Yuan, H. / Sun, M.F. / Wang, Y.H. / Liao, S.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ksr.cif.gz | 276.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ksr.ent.gz | 186.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ksr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ksr_validation.pdf.gz | 848.3 KB | Display | wwPDB validaton report |
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Full document | 6ksr_full_validation.pdf.gz | 851.1 KB | Display | |
Data in XML | 6ksr_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 6ksr_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/6ksr ftp://data.pdbj.org/pub/pdb/validation_reports/ks/6ksr | HTTPS FTP |
-Related structure data
Related structure data | 5hexS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50495.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eimeria tenella (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: A0A172WCE4, UniProt: U6KUE1*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Sugar | ChemComp-GLA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2000mM Ammonium sulfate, 100mM Sodium cacodylate/Hydrochloric acid pH 6.5, 200mM Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→45.88 Å / Num. obs: 231302 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.47 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Χ2: 0.94 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.37→1.41 Å / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8139 / Rpim(I) all: 0.604 / Χ2: 1.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HEX Resolution: 1.37→45.88 Å / SU ML: 0.1295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1655
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→45.88 Å
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Refine LS restraints |
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LS refinement shell |
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