+Open data
-Basic information
Entry | Database: PDB / ID: 4ow8 | ||||||
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Title | Crystal structure of kinase domain of PknA from Mtb | ||||||
Components | Serine/threonine-protein kinase PknA | ||||||
Keywords | TRANSFERASE / PknA / kinase / drug target / Mtb | ||||||
Function / homology | Function and homology information biological process involved in interaction with host => GO:0051701 / peptidyl-threonine autophosphorylation / negative regulation of lipid biosynthetic process / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / positive regulation of catalytic activity / : / positive regulation of DNA binding / regulation of cell shape / protein autophosphorylation ...biological process involved in interaction with host => GO:0051701 / peptidyl-threonine autophosphorylation / negative regulation of lipid biosynthetic process / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / positive regulation of catalytic activity / : / positive regulation of DNA binding / regulation of cell shape / protein autophosphorylation / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Ravala, S.K. / Singh, S. / Yadav, G.S. / Karthikeyan, S. / Chakraborti, P.K. | ||||||
Funding support | India, 1items
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Citation | Journal: Febs J. / Year: 2015 Title: Evidence that phosphorylation of threonine in the GT motif triggers activation of PknA, a eukaryotic-type serine/threonine kinase from Mycobacterium tuberculosis. Authors: Ravala, S.K. / Singh, S. / Yadav, G.S. / Kumar, S. / Karthikeyan, S. / Chakraborti, P.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ow8.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ow8.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ow8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/4ow8 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4ow8 | HTTPS FTP |
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-Related structure data
Related structure data | 1o6yS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30449.021 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 1-283) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT0018,MTCY10H4.15c,RV0015c,pknA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P65726, UniProt: P9WI83*PLUS, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.25 M NaCl, 1.1 M (NH4)2SO4, 0.1 M Bis-Tris (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 24, 2013 / Details: Varimax Optics |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→46.84 Å / Num. all: 15916 / Num. obs: 15916 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.057 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 10.3 / Rsym value: 0.238 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O6Y Resolution: 2.03→46.84 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 6.247 / SU ML: 0.171 / Data cutoff high absF: 46.84 / Data cutoff low absF: 2.03 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.41 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→46.84 Å
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Refine LS restraints |
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