+Open data
-Basic information
Entry | Database: PDB / ID: 6k8z | ||||||
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Title | Pyridoxal Kinase from Leishmania donovani in complex with ADP | ||||||
Components | Pyridoxal kinase, putative | ||||||
Keywords | TRANSFERASE / Nucleotide binding / ATP binding / Kinase activity / Metal binding | ||||||
Function / homology | Function and homology information pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Are, S. / Gatreddi, S. / Qureshi, I.A. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani. Authors: Are, S. / Gatreddi, S. / Jakkula, P. / Qureshi, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k8z.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k8z.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/6k8z ftp://data.pdbj.org/pub/pdb/validation_reports/k8/6k8z | HTTPS FTP |
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-Related structure data
Related structure data | 6k90C 6k91C 6k92C 1lhpS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35341.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: LdCL_300018300 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S7X3C0, pyridoxal kinase |
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-Non-polymers , 5 types, 228 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 18% PEG 8000, 0.1M Sodium Cacodylate, 0.32M Calcium Acetate, 4% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.98 Å / Num. obs: 44763 / % possible obs: 97.2 % / Redundancy: 3.6 % / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 2822 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LHP Resolution: 1.9→42.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.233 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.139 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.141 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→42.98 Å
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Refine LS restraints |
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