[English] 日本語
Yorodumi- PDB-6i2p: Crystal structure of the Mycobacterium tuberculosis PknB kinase d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i2p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in complex with its substrate GarA | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / kinase / FHA-domain protein | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Andre-Leroux, G. / Hindie, V. / Barilone, N. / Bellinzoni, M. / Alzari, P.M. | ||||||
Citation | Journal: Sci.Signal. / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i2p.cif.gz | 310.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i2p.ent.gz | 249.9 KB | Display | PDB format |
PDBx/mmJSON format | 6i2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i2p_validation.pdf.gz | 1021.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6i2p_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6i2p_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 6i2p_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/6i2p ftp://data.pdbj.org/pub/pdb/validation_reports/i2/6i2p | HTTPS FTP |
-Related structure data
Related structure data | 6i2qC 6i2rC 6i2sC 1o6yS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pknB, Rv0014c, MTCY10H4.14c / Production host: Escherichia coli BL21(DE3) (bacteria) 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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: garA, Rv1827, MTCY1A11.16c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WJA9 |
---|
-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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
---|
-Non-polymers , 4 types, 235 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9763 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.42 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.37→38.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.37→2.44 Å / Total num. of bins used: 18
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|