+Open data
-Basic information
Entry | Database: PDB / ID: 3b8a | ||||||
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Title | Crystal structure of yeast hexokinase PI in complex with glucose | ||||||
Components | Hexokinase-1 | ||||||
Keywords | TRANSFERASE / induced fit / Allosteric enzyme / ATP-binding / Glycolysis / Kinase / Nucleotide-binding / Phosphorylation | ||||||
Function / homology | Function and homology information fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process ...fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / glucose binding / fructose metabolic process / glucose import / intracellular glucose homeostasis / Neutrophil degranulation / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å | ||||||
Authors | Kuser, P. / Cupri, F. / Bleicher, L. / Polikarpov, I. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of yeast hexokinase PI in complex with glucose: A classical "induced fit" example revised. Authors: Kuser, P. / Cupri, F. / Bleicher, L. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b8a.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b8a.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 3b8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/3b8a ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b8a | HTTPS FTP |
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-Related structure data
Related structure data | 1ig8S 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: 53804.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04806, hexokinase |
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#2: Sugar | ChemComp-BGC / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 3.29 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 277 K / Method: hanging drop / pH: 6.5 Details: 30% PEG 4000, 0.1M phosphate buffer, 10 mg/ml protein concentration, pH 6.5, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 1999 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→12.92 Å / Num. all: 14357 / Num. obs: 14357 / % possible obs: 92.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 47.358 Å2 / Rsym value: 0.119 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1007 / Rsym value: 0.477 / % possible all: 94.44 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1IG8 Resolution: 2.95→12.92 Å / FOM work R set: 0.828 / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ml Details: Used group refinement for B-factors (one per residue)
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Solvent computation | Bsol: 24.278 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.45 Å2 / Biso mean: 44.81 Å2 / Biso min: 16.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→12.92 Å
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Refine LS restraints |
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