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Yorodumi- PDB-3f69: Crystal structure of the Mycobacterium tuberculosis PknB mutant k... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f69 | ||||||
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Title | Crystal structure of the Mycobacterium tuberculosis PknB mutant kinase domain in complex with KT5720 | ||||||
Components | Serine/threonine-protein kinase pknB | ||||||
Keywords | TRANSFERASE / protein kinase / PknB / Mycobacterium tuberculosis / KT5720 / Structural Genomics / Structual Genomics / Cocrystallization of PknB kinase domain and inhibitors / TB Structural Genomics Consortium / TBSGC / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase | ||||||
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 / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall ...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 / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion 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 / ATP binding / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Alber, T. / Mieczkowski, C.A. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase. Authors: Mieczkowski, C. / Iavarone, A.T. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f69.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f69.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f69 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f69 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33550.484 Da / Num. of mol.: 2 / Fragment: PknB mutant kinase domain / Mutation: L33D, M145L, M155V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0017, MTCY10H4.14c, pknB, Rv0014c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon plus References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 4.09 Å3/Da / Density % sol: 69.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 25% PEG 3350, 200 mM ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11586 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2007 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11586 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 28331 / % possible obs: 100 % / Redundancy: 32.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 49.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 32.7 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PknB Leu33Asp kinase domain (1-308) Resolution: 2.8→39.78 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0 / SU B: 26.189 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.307 / 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: 25.529 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.512 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.801→2.874 Å / Total num. of bins used: 20
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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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