+Open data
-Basic information
Entry | Database: PDB / ID: 5zqt | ||||||
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Title | Crystal structure of Oryza sativa hexokinase 6 | ||||||
Components | Hexokinase-6 | ||||||
Keywords | TRANSFERASE / hexokinase | ||||||
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: 2.84 Å | ||||||
Authors | Matsudaira, K. / Mochizuki, S. / Yoshida, H. / Kamitori, S. / Akimitsu, K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Oryza sativa hexokinase 6 Authors: Matsudaira, K. / Mochizuki, S. / Yoshida, H. / Kamitori, S. / Akimitsu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zqt.cif.gz | 269.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zqt.ent.gz | 215.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/5zqt ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zqt | HTTPS FTP |
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-Related structure data
Related structure data | 4qs7S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 51867.008 Da / Num. of mol.: 3 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 #2: Chemical | #3: Chemical | #4: Sugar | #5: 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: 3.03 Å3/Da / Density % sol: 59.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M MOPSO, 0.1 M Bis-Tris, 5%w/v PEG20000, 25% w/v Trimethypropane, 1% w/v NDSB195, 0.1 M Spermine tetrahydrochloride, 0.1 M Spermidine trihydrochloride, 0.1 M 1,4-Diaminobutane ...Details: 0.1 M MOPSO, 0.1 M Bis-Tris, 5%w/v PEG20000, 25% w/v Trimethypropane, 1% w/v NDSB195, 0.1 M Spermine tetrahydrochloride, 0.1 M Spermidine trihydrochloride, 0.1 M 1,4-Diaminobutane dihydrochloride, 0.1 M DL-Ornithine monohydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→48.79 Å / Num. obs: 45291 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 30.56 |
Reflection shell | Resolution: 2.84→2.91 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.535 / Num. unique obs: 3318 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QS7 Resolution: 2.84→48.79 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.085 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 18.351 / ESU R Free: 0.384 / 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: 54.845 Å2
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Refinement step | Cycle: 1 / Resolution: 2.84→48.79 Å
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Refine LS restraints |
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