+Open data
-Basic information
Entry | Database: PDB / ID: 6krj | ||||||
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Title | Crystal structure of Hexokinase | ||||||
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: 1.72 Å | ||||||
Authors | Sun, M.F. / Wang, Y.H. / Liao, S.Q. / Yuan, H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Hexokinase Authors: Sun, M.F. / Wang, Y.H. / Liao, S.Q. / Yuan, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6krj.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6krj.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 6krj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6krj_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 6krj_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 6krj_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 6krj_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6krj ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6krj | 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 BL21(DE3) (bacteria) References: UniProt: A0A172WCE4, UniProt: U6KUE1*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200mM Calcium acetate hydrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 61084 / % possible obs: 99.57 % / Redundancy: 7.6 % / Biso Wilson estimate: 33.68 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.021 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.78→1.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 62194 / Rpim(I) all: 0.248 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HEX Resolution: 1.72→37.17 Å / SU ML: 0.2263 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.4742
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→37.17 Å
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Refine LS restraints |
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LS refinement shell |
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