[English] 日本語
Yorodumi- PDB-6q91: Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q91 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide | ||||||
Components | Galactokinase | ||||||
Keywords | TRANSFERASE / GALK1 / fragment / fragment-bound / galactokinase 1 / sugar kinase | ||||||
Function / homology | Function and homology information glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose binding / galactose metabolic process / galactose catabolic process via UDP-galactose ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose binding / galactose metabolic process / galactose catabolic process via UDP-galactose / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. ...Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / Lai, K. / Yue, W.W. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide Authors: Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / Lai, K. / Yue, W.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6q91.cif.gz | 296.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6q91.ent.gz | 236.5 KB | Display | PDB format |
PDBx/mmJSON format | 6q91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q91_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6q91_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6q91_validation.xml.gz | 59.8 KB | Display | |
Data in CIF | 6q91_validation.cif.gz | 82.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q91 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q91 | HTTPS FTP |
-Related structure data
Related structure data | 1wuuS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42209.973 Da / Num. of mol.: 4 / Mutation: K252A, E253A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Production host: Escherichia coli (E. coli) / References: UniProt: P51570, galactokinase #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-HR8 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MOPS/sodium HEPES, 40-50% Morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M morpheus carboxylic acids mix (0.02M each of sodium formate, ammonium ...Details: 0.1M MOPS/sodium HEPES, 40-50% Morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M morpheus carboxylic acids mix (0.02M each of sodium formate, ammonium actetate, sodium citrate tribasic dihydrate, sodium oxamate, potassium sodium tartrate tetrahydrate PH range: 7-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.27→82.74 Å / Num. obs: 91197 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.131 / Net I/σ(I): 4.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wuu Resolution: 2.4→82.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.165 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.277 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.38 Å2 / Biso mean: 44.518 Å2 / Biso min: 15.79 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→82.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|