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Yorodumi- PDB-4f9o: Crystal Structure of recombinant human Hexokinase type I with 2-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f9o | ||||||
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Title | Crystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate | ||||||
Components | Hexokinase-1 | ||||||
Keywords | TRANSFERASE / hexokinase / 2-deoxy Glucose-6-Phosphate | ||||||
Function / homology | Function and homology information Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / hexokinase activity / mannokinase activity / maintenance of protein location in mitochondrion / positive regulation of cytokine production involved in immune response / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation ...Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / hexokinase activity / mannokinase activity / maintenance of protein location in mitochondrion / positive regulation of cytokine production involved in immune response / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / peptidoglycan binding / glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / positive regulation of interleukin-1 beta production / glycolytic process / glucose metabolic process / mitochondrial outer membrane / inflammatory response / membrane raft / innate immune response / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Shen, L. / Honzatko, R.B. | ||||||
Citation | Journal: to be published Title: Inhibitor Sites of Unequal Affinity Linked by Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I Authors: Shen, L. / Gao, Y. / Honzatko, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f9o.cif.gz | 362.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f9o.ent.gz | 292.3 KB | Display | PDB format |
PDBx/mmJSON format | 4f9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/4f9o ftp://data.pdbj.org/pub/pdb/validation_reports/f9/4f9o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 102379.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HK1 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19367, hexokinase |
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-Sugars , 2 types, 8 molecules
#2: Sugar | ChemComp-BGC / #3: Sugar | ChemComp-0NZ / |
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-Non-polymers , 3 types, 309 molecules
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CIT / | #6: 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: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 277 K / Method: hanging drop / pH: 6 Details: PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→35.36 Å / Num. obs: 69139 / % possible obs: 99.3 % / Redundancy: 3.82 % / Rmerge(I) obs: 0.086 / Χ2: 0.95 / Net I/σ(I): 8.4 / Scaling rejects: 2000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→35.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.561 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.911 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.61 Å2 / Biso mean: 55.3717 Å2 / Biso min: 16.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→35.36 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7102 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.65→2.718 Å / Total num. of bins used: 20
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