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Yorodumi- PDB-5e10: Crystal Structure of PASTA Domains 1 and 2 of Mycobacterium tuber... -
+Open data
-Basic information
Entry | Database: PDB / ID: 50000000000 | ||||||
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Title | Crystal Structure of PASTA Domains 1 and 2 of Mycobacterium tuberculosis Protein Kinase B | ||||||
Components | Serine/threonine-protein kinase PknB | ||||||
Keywords | TRANSFERASE / kinase / extracellular sensor domain / peptidoglycan binding / Structural Genomics / 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 / peptidoglycan-based cell wall / negative regulation of protein binding ...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 / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion 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 / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å | ||||||
Authors | Prigozhin, D.M. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site. Authors: Prigozhin, D.M. / Papavinasasundaram, K.G. / Baer, C.E. / Murphy, K.C. / Moskaleva, A. / Chen, T.Y. / Alber, T. / Sassetti, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e10.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e10.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e10 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e10 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13717.271 Da / Num. of mol.: 1 / Fragment: UNP residues 360-491 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pknB, Rv0014c, MTCY10H4.14c / Production host: Escherichia coli (E. coli) References: UniProt: P9WI81, non-specific serine/threonine protein kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1 M CHES pH 9.5, 30% isopropanol, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→41.995 Å / Num. obs: 13502 / % possible obs: 100 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.28 Å2 / Rmerge(I) obs: 0.09 / Χ2: 0.98 / Net I/av σ(I): 14.797 / Net I/σ(I): 7.3 / Num. measured all: 52681 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→41.995 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.6 Å2 / Biso mean: 22.9223 Å2 / Biso min: 9.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→41.995 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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