+Open data
-Basic information
Entry | Database: PDB / ID: 6yjz | ||||||
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Title | Crystal structure of mouse pyridoxal kinase in apo form | ||||||
Components | Pyridoxal Kinase | ||||||
Keywords | TRANSFERASE / PDXK / PLP / PL / Vitamin B6 / Enzyme | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Kasaragod, V.B. / Schindelin, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission. Authors: Kasaragod, V.B. / Pacios-Michelena, A. / Schaefer, N. / Zheng, F. / Bader, N. / Alzheimer, C. / Villmann, C. / Schindelin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yjz.cif.gz | 450.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yjz.ent.gz | 377.2 KB | Display | PDB format |
PDBx/mmJSON format | 6yjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yjz ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yjz | HTTPS FTP |
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-Related structure data
Related structure data | 6yk0C 6yk1C 2xytS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35212.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.99 Å3/Da / Density % sol: 58.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18-0.24 M sodium thiocyanate and 18-26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.32 Å / Num. obs: 57180 / % possible obs: 95.6 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.093 / Rrim(I) all: 0.08752 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.45→2.53 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5965 / CC1/2: 0.572 / Rpim(I) all: 0.7 / Rrim(I) all: 0.6776 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XYT Resolution: 2.45→47.32 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.32 Å
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Refine LS restraints |
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LS refinement shell |
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