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Yorodumi- PDB-1mru: Intracellular Ser/Thr protein kinase domain of Mycobacterium tube... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mru | ||||||
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Title | Intracellular Ser/Thr protein kinase domain of Mycobacterium tuberculosis PknB. | ||||||
Components | Probable serine/threonine-protein kinase pknB | ||||||
Keywords | TRANSFERASE / regulatory / ATP-recognition / molecular evolution / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / 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 / MAD / Resolution: 3 Å | ||||||
Authors | Young, T.A. / Delagoutte, B. / Endrizzi, J.A. / Alber, T. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases. Authors: Young, T.A. / Delagoutte, B. / Endrizzi, J.A. / Falick, A.M. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mru.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mru.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/1mru ftp://data.pdbj.org/pub/pdb/validation_reports/mr/1mru | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33518.676 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pet28b / Cell line (production host): bl21 (de3) / Production host: Escherichia coli (E. coli) References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | ChemComp-MG / #3: Chemical | |
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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: 2.61 Å3/Da / Density % sol: 52.82 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, sodium acetate, Tris-HCl, spermine, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 8.3.1 / Wavelength: 1.1000, 0.9798 | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2002 | |||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3→50 Å / Num. all: 13890 / Num. obs: 13890 / % possible obs: 99 % / Observed criterion σ(F): 3.78 / Observed criterion σ(I): 14.3 | |||||||||
Reflection shell | Resolution: 3→3.1 Å / % possible all: 99 | |||||||||
Reflection | *PLUS Lowest resolution: 110 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.043 | |||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 7.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→29.68 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.428 Å2 / ksol: 0.301367 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.67 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→29.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.2959 / Rfactor Rwork: 0.2365 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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