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- PDB-6i2p: Crystal structure of the Mycobacterium tuberculosis PknB kinase d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i2p | ||||||
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Title | Crystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in complex with its substrate GarA | ||||||
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![]() | SIGNALING PROTEIN / kinase / FHA-domain protein | ||||||
Function / homology | ![]() negative regulation of growth rate / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / regulation of cellular respiration / negative regulation of glycolytic process / positive regulation of catalytic activity / molecular function inhibitor activity / positive regulation of DNA binding ...negative regulation of growth rate / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / regulation of cellular respiration / negative regulation of glycolytic process / positive regulation of catalytic activity / molecular function inhibitor activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / regulation of cell shape / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / extracellular region / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Andre-Leroux, G. / Hindie, V. / Barilone, N. / Bellinzoni, M. / Alzari, P.M. | ||||||
![]() | ![]() Title: Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling. Authors: Wagner, T. / Andre-Leroux, G. / Hindie, V. / Barilone, N. / Lisa, M.N. / Hoos, S. / Raynal, B. / Vulliez-Le Normand, B. / O'Hare, H.M. / Bellinzoni, M. / Alzari, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.7 KB | Display | ![]() |
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PDB format | ![]() | 249.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6i2qC ![]() 6i2rC ![]() 6i2sC ![]() 1o6yS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABDE
#1: Protein | Mass: 30520.119 Da / Num. of mol.: 2 / Mutation: L33E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: pknB, Rv0014c, MTCY10H4.14c / Production host: ![]() ![]() References: UniProt: P9WI81, non-specific serine/threonine protein kinase #2: Protein | Mass: 17322.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: garA, Rv1827, MTCY1A11.16c / Production host: ![]() ![]() |
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-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 4 types, 235 molecules ![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM Hepes-Na pH 7.5, 4 % w/v PEG 400, 2 M (NH4)2SO4, 4 mM AMP-PCP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→38.85 Å / Num. obs: 36716 / % possible obs: 96.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 67.39 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.04 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.37→2.46 Å / Rmerge(I) obs: 0.439 / Rpim(I) all: 0.235 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1O6Y Resolution: 2.37→38.85 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.378 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.227
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Displacement parameters | Biso mean: 67.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.37→38.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.44 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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