+Open data
-Basic information
Entry | Database: PDB / ID: 2f7k | ||||||
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Title | Crystal Structure of Human Pyridoxal Kinase | ||||||
Components | Pyridoxal kinase | ||||||
Keywords | TRANSFERASE / ALPHA-BETA STRUCTURE | ||||||
Function / homology | Function and homology information pyridoxal metabolic process / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / sodium ion binding / potassium ion binding / specific granule lumen ...pyridoxal metabolic process / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / sodium ion binding / potassium ion binding / specific granule lumen / pyridoxal phosphate binding / secretory granule lumen / phosphorylation / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jiang, T. / Cao, P. / Gong, Y. / Tang, L. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2006 Title: Crystal structure of human pyridoxal kinase Authors: Cao, P. / Gong, Y. / Tang, L. / Leung, Y.C. / Jiang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f7k.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f7k.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 2f7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/2f7k ftp://data.pdbj.org/pub/pdb/validation_reports/f7/2f7k | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37067.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pReceiver-B01a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) plysS / References: UniProt: O00764, pyridoxal kinase #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: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8M Ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 11, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. all: 24880 / Num. obs: 24880 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.03 |
Reflection shell | Resolution: 2.6→2.66 Å / Rmerge(I) obs: 0.306 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: This is a twinned structure. The twinning operator is (h,k,l) -> (h,-k,-l) and the twinning fraction is 0.47.
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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LS refinement shell | Resolution: 2.8→2.87 Å /
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