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Yorodumi- PDB-4esq: Crystal structure of the extracellular domain of PknH from Mycoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4esq | ||||||
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Title | Crystal structure of the extracellular domain of PknH from Mycobacterium tuberculosis | ||||||
Components | Serine/threonine protein kinaseSerine/threonine-specific protein kinase | ||||||
Keywords | TRANSFERASE / Receptor Kinase / Membrane | ||||||
Function / homology | Function and homology information regulation of lipid biosynthetic process / negative regulation of growth / negative regulation of catalytic activity / response to host immune response / cell wall / positive regulation of catalytic activity / plasma membrane => GO:0005886 / positive regulation of DNA binding / protein autophosphorylation / membrane => GO:0016020 ...regulation of lipid biosynthetic process / negative regulation of growth / negative regulation of catalytic activity / response to host immune response / cell wall / positive regulation of catalytic activity / plasma membrane => GO:0005886 / positive regulation of DNA binding / protein autophosphorylation / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Cavazos, A. / Prigozhin, D.M. / Alber, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structure of the sensor domain of Mycobacterium tuberculosis PknH receptor kinase reveals a conserved binding cleft. Authors: Cavazos, A. / Prigozhin, D.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 | 4esq.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4esq.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 4esq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/4esq ftp://data.pdbj.org/pub/pdb/validation_reports/es/4esq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20661.994 Da / Num. of mol.: 1 / Fragment: unp residues 83332-83523 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pknH, Rv1266c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: A5U1W4, UniProt: P9WI71*PLUS | ||
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#2: Chemical | ChemComp-BTB / | ||
#3: Chemical | #4: 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: 2.01 Å3/Da / Density % sol: 38.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.5 Details: 0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG 3350, 50mM terbium nitrate, pH 5.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.8 % / Av σ(I) over netI: 17.44 / Number: 69365 / Rmerge(I) obs: 0.061 / Χ2: 1.01 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 18089 / % possible obs: 98.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.7→50 Å / Num. obs: 34200 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Χ2: 1.015 / Net I/σ(I): 17.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD | ||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.69 / FOM acentric: 0.71 / FOM centric: 0.51 / Reflection: 8491 / Reflection acentric: 7763 / Reflection centric: 728 | ||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→48.784 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.934 Å2 / ksol: 0.317 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.6 Å2 / Biso mean: 18.0416 Å2 / Biso min: 7.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→48.784 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: 12
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