+Open data
-Basic information
Entry | Database: PDB / ID: 6jj4 | ||||||
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Title | Crystal structure of OsHXK6-apo form | ||||||
Components | Hexokinase-6 | ||||||
Keywords | STRUCTURAL PROTEIN / Hexokinase ATP phosphorylation | ||||||
Function / homology | Function and homology information chloroplast outer membrane / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-glucose binding / intracellular glucose homeostasis / response to glucose / glycolytic process ...chloroplast outer membrane / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-glucose binding / intracellular glucose homeostasis / response to glucose / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | He, C. / Wei, P. / Chen, J. / Wang, H. / Wan, Y. / Zhou, J. / Zhu, Y. / Huang, W. / Yin, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of OsHXK6-apo Authors: He, C. / Wei, P. / Chen, J. / Wang, H. / Wan, Y. / Zhou, J. / Zhu, Y. / Huang, W. / Yin, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jj4.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jj4.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jj4 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jj4 | HTTPS FTP |
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-Related structure data
Related structure data | 4qs8S 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: 51291.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: HXK6, HXK2, Os01g0742500, LOC_Os01g53930, P0439E07.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LQ68, hexokinase |
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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: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium tartrate dibasic, and 20% (w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 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: 2.6→40.28 Å / Num. obs: 13424 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.02669 / Net I/σ(I): 14.81 |
Reflection shell | Resolution: 2.6→2.693 Å / Rmerge(I) obs: 0.05874 / Mean I/σ(I) obs: 8.16 / Num. unique obs: 1324 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QS8 Resolution: 2.6→40.28 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40.28 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -34.0063 Å / Origin y: 13.2218 Å / Origin z: -12.4851 Å
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Refinement TLS group | Selection details: all |