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Yorodumi- PDB-1cza: MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cza | ||||||
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Title | MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE, GLUCOSE-6-PHOSPHATE, AND ADP | ||||||
Components | HEXOKINASE TYPE I | ||||||
Keywords | TRANSFERASE / STRUCTURALLY HOMOLOGOUS DOMAINS | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Aleshin, A.E. / Liu, X. / Kirby, C. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation. Authors: Aleshin, A.E. / Kirby, C. / Liu, X. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Regulation of Hexokinase I: Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Phosphate Authors: Aleshin, A.E. / Zeng, C. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cza.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cza.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 1cza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cza_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1cza_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1cza_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 1cza_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1cza ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1cza | HTTPS FTP |
-Related 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: 102587.008 Da / Num. of mol.: 1 / Mutation: E280A, R283A, G284Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: NEURON / Organ: BRAIN / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P19367, hexokinase | ||||||||
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#2: Sugar | #3: Sugar | #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | Compound details | WILD-TYPE HEXOKINASE I IS A MONOMER AT CONCENTRATION BELOW 1 MG/ML. THE MUTANT IN THIS ENTRY IS A ...WILD-TYPE HEXOKINASE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.11 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: PEG 8000, SODIUM ACETATE, MES, ADP, ALUMINUM NITRATE, SODIUM FLUORIDE, MAGNESIUM ACETATE, GLUCOSE, pH 6.5, EVAPORATION, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→17 Å / Num. all: 96631 / Num. obs: 96631 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / % possible all: 98.3 |
Reflection | *PLUS Num. obs: 83349 / % possible obs: 98.6 % / Num. measured all: 286697 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 82.3 % / Rmerge(I) obs: 0.41 |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION ADP is bound near the N-terminus of the polypeptide chain. Side chains of residues 16, 20, 24, 101, 102, 353, 794, 801, ...Details: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION ADP is bound near the N-terminus of the polypeptide chain. Side chains of residues 16, 20, 24, 101, 102, 353, 794, 801, 811 have poor electron density. Their occupancies are set to 0.01.
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.268 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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