+Open data
-Basic information
Entry | Database: PDB / ID: 1o6y | ||||||
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Title | Catalytic domain of PknB kinase from Mycobacterium tuberculosis | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE PKNB | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE PROTEIN KINASE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Ortiz-Lombardia, M. / Pompeo, F. / Boitel, B. / Alzari, P.M. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure of the Catalytic Domain of the Pknb Serine/Threonine Kinase from Mycobacterium Tuberculosis Authors: Ortiz-Lombardia, M. / Pompeo, F. / Boitel, B. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o6y.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o6y.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1o6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/1o6y ftp://data.pdbj.org/pub/pdb/validation_reports/o6/1o6y | HTTPS FTP |
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-Related structure data
Related structure data | 1phkS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32458.506 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-279 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: INSTITUT PASTEUR COLLECTION / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-ACP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUES IN THE N-TERMINAL TAG (1-22) ARE DISORDERED. SIXTEEN RESIDUES (164-179) IN THE ACTIVATION ...RESIDUES IN THE N-TERMINAL TAG (1-22) ARE DISORDERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.17 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PROTEIN CRYSTALLIZED FROM 27% PEG 400, 4% 1,3-BUTANEDIOL, 100 MM HEPES, PH 7.5, 30 MM MGCL2 AT 19 DEGREES C | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60.86 Å / Num. obs: 17152 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.3 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 61 Å / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHK Resolution: 2.2→61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.608 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.841 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→61 Å
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