[English] 日本語
Yorodumi- PDB-1hkb: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hkb | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND GLUCOSE-6-PHOSPHATE | ||||||
Components | D-GLUCOSE 6-PHOSPHOTRANSFERASE | ||||||
Keywords | PHOSPHOTRANSFERASE / GLYCOLYSIS / ALLOSTERIC ENZYME / GLUCOSE / GLUCOSE-6-PHOSPHATE | ||||||
Function / homology | Function and homology information Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / hexokinase activity / maintenance of protein location in mitochondrion / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase / positive regulation of cytokine production involved in immune response / fructokinase activity / carbohydrate phosphorylation ...Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / hexokinase activity / maintenance of protein location in mitochondrion / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase / positive regulation of cytokine production involved in immune response / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / peptidoglycan binding / D-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: 2.8 Å | ||||||
Authors | Aleshin, A.E. / Zeng, C. / Burenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The mechanism of regulation of hexokinase: new insights from the crystal structure of recombinant human brain hexokinase complexed with glucose and glucose-6-phosphate. Authors: Aleshin, A.E. / Zeng, C. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B. #1: Journal: FEBS Lett. / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of Human Brain Hexokinase Authors: Aleshin, A.E. / Zeng, C. / Fromm, H.J. / Honzatko, R.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1hkb.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1hkb.ent.gz | 292.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hkb_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1hkb_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1hkb_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 1hkb_validation.cif.gz | 62.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hkb ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hkb | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.999648, -0.026325, -0.003239), Vector: |
-Components
#1: Protein | Mass: 102625.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CRYSTALLIZES AS A DIMER IN ASYMMETRIC UNIT / Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Organ: BRAIN / Plasmid: PET-11A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19367, hexokinase #2: Sugar | ChemComp-BGC / #3: Sugar | ChemComp-G6P / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Compound details | THE COMPLEX OF BRAIN HEXOKINASE WITH GLC AND G6P CRYSTALLIZES AS A HOMODIMER. EACH SUBUNIT (CHAINS ...THE COMPLEX OF BRAIN HEXOKINASE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.6 Details: HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF ...Details: HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION; THEN SOAKED WITH 10 MM G6P AND 5 MM GLUCOSE. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop was combined with an equal volume of reservoir solution | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→38 Å / Num. obs: 113243 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 62.4 Å2 / Rsym value: 0.055 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.32 / % possible all: 88 |
Reflection | *PLUS Num. measured all: 58613 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 88 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: YEAST HEXOKINASE COMPLEXED WITH GLUCOSE (BARTUNIK, UNPUBLISHED) Resolution: 2.8→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: TOPOLOGY AND ENERGY PARAMETERS FOR GLUCOSE-6-PHOSPHATE WERE BUILT BY ANALOGY TO THOSE OF GLUCOSE AND ARE PRESENTED IN FILES PAR.HK AND TOP.HK
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.06 Å / Weight Biso : 4 / Weight position: 100
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.308 |