+Open data
-Basic information
Entry | Database: PDB / ID: 2yxu | ||||||
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Title | Human Pyridoxal Kinase | ||||||
Components | Pyridoxal kinase | ||||||
Keywords | TRANSFERASE / beta sheet with alpha helix / ATP complex / metal ion | ||||||
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: 2.2 Å | ||||||
Authors | Safo, M.K. / Musayev, F.N. / Ko, T.P. / Schirch, V. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. Authors: Musayev, F.N. / di Salvo, M.L. / Ko, T.P. / Gandhi, A.K. / Goswami, A. / Schirch, V. / Safo, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yxu.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yxu.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yxu ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yxu | HTTPS FTP |
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-Related structure data
Related structure data | 2yxtSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35143.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDXK, PKH, PNK / Plasmid: pET 22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O00764, pyridoxal kinase |
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-Non-polymers , 6 types, 497 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Chemical | ChemComp-MPD / ( #7: 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: 3.15 Å3/Da / Density % sol: 60.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2mM MgATP, 20mM K-PO4 (pH 7.0), 100mM NaCl, 100mM Tris-HCl (pH 8.0), 50% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 11, 2006 / Details: MSC Varimax confocal optics |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 45398 / Num. obs: 44337 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 5.2 / Num. unique all: 4452 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YXT Resolution: 2.2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.027
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