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Yorodumi- PDB-5m06: Crystal structure of Mycobacterium tuberculosis PknI kinase domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m06 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis PknI kinase domain | ||||||
Components | Serine/threonine-protein kinase PknI | ||||||
Keywords | SIGNALING PROTEIN / Tuberculosis / kinase / signalling | ||||||
Function / homology | Function and homology information regulation of growth rate / peptidyl-threonine phosphorylation / manganese ion binding / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...regulation of growth rate / peptidyl-threonine phosphorylation / manganese ion binding / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wagner, T. / Lisa, M.N. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M. | ||||||
Citation | Journal: FEBS J. / Year: 2017 Title: The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation. Authors: Lisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m06.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m06.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 5m06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m06_validation.pdf.gz | 748.3 KB | Display | wwPDB validaton report |
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Full document | 5m06_full_validation.pdf.gz | 749.5 KB | Display | |
Data in XML | 5m06_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5m06_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m06 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m06 | HTTPS FTP |
-Related 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: 29670.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: pknI, Rv2914c, MTCY338.02c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WI69, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ADP / | #3: Chemical | ChemComp-CA / | #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: 2.26 Å3/Da / Density % sol: 45.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18% PEG 4000, 240 mM CaCl2, 100 mM Tris-HCl pH 8.5, 5 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.43 Å / Num. obs: 36891 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 48.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / CC1/2: 0.668 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Partially refined model from SeMet MAD phasing on a nonisomorphous crystal Resolution: 2→28.09 Å / Cor.coef. Fo:Fc: 0.9511 / Cor.coef. Fo:Fc free: 0.9444 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.154
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Displacement parameters | Biso mean: 62.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→28.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.06 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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