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Yorodumi- PDB-4x3f: Crystal structure of the intracellular domain of the M. tuberculo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x3f | ||||||
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Title | Crystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA | ||||||
Components | (Serine/threonine-protein kinase PknA) x 3 | ||||||
Keywords | TRANSFERASE / Kinase / autoinhibition / phosphorylation | ||||||
Function / homology | Function and homology information 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 / non-specific serine/threonine protein kinase / protein kinase activity ...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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wagner, T. / Wehenkel, A. / Alzari, P.M. / Bellinzoni, M. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis shows an Src-like autoinhibited conformation. Authors: Wagner, T. / Alexandre, M. / Duran, R. / Barilone, N. / Wehenkel, A. / 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 | 4x3f.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x3f.ent.gz | 261 KB | Display | PDB format |
PDBx/mmJSON format | 4x3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x3f ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x3f | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 36017.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WI83, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 35937.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WI83, non-specific serine/threonine protein kinase |
#3: Protein | Mass: 35857.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WI83, non-specific serine/threonine protein kinase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 63.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4.3 M NaCl, 0.1 M Hepes-Na pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→43.6 Å / Num. obs: 31961 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.197 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1o6y Resolution: 2.9→43.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 46.23 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.32 / 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: 91.212 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→43.56 Å
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Refine LS restraints |
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