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Yorodumi- PDB-3b3l: Crystal structures of alternatively-spliced isoforms of human ket... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b3l | ||||||
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Title | Crystal structures of alternatively-spliced isoforms of human ketohexokinase | ||||||
Components | KetohexokinaseHepatic fructokinase | ||||||
Keywords | TRANSFERASE / Fructose kinase / Carbohydrate metabolism / Disease mutation / Phosphorylation | ||||||
Function / homology | Function and homology information Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Trinh, C.H. / Asipu, A. / Bonthron, D.T. / Phillips, S.E.V. | ||||||
Citation | Journal: To be Published Title: Crystal structures of alternatively-spliced isoforms of human ketohexokinase Authors: Trinh, C.H. / Asipu, A. / Bonthron, D.T. / Phillips, S.E.V. | ||||||
History |
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Remark 999 | SEQUENCE The sequence is based on the isoform c in the database, KHK_HUMAN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b3l.cif.gz | 225.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b3l.ent.gz | 183.3 KB | Display | PDB format |
PDBx/mmJSON format | 3b3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b3l ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b3l | HTTPS FTP |
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-Related structure data
Related structure data | 2hqqS 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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Unit cell |
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-Components
#1: Protein | Mass: 32561.982 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P50053, ketohexokinase #2: 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: 4.38 Å3/Da / Density % sol: 71.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 20% PEG 3000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 optimised for 1.488 angstrom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→110.432 Å / Num. all: 49962 / Num. obs: 49962 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7208 / Rsym value: 0.354 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HQQ Resolution: 2.9→25.38 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.88 / SU B: 31.049 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.577 / ESU R Free: 0.355 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.154 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→25.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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