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- PDB-5m08: Crystal structure of Mycobacterium tuberculosis PknI kinase domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m08 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis PknI kinase domain, C20A_R136A double mutant | ||||||
![]() | Serine/threonine-protein kinase PknI | ||||||
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Function / homology | ![]() regulation of growth rate / peptidyl-threonine phosphorylation / manganese ion binding / peptidyl-serine phosphorylation / protein autophosphorylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M. | ||||||
![]() | ![]() Title: The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation. Authors: Lisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.3 KB | Display | ![]() |
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PDB format | ![]() | 162.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5m06C ![]() 5m07SC ![]() 5m09C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29552.297 Da / Num. of mol.: 2 / Mutation: C20A,R136A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 25618 / H37Rv / Gene: pknI, Rv2914c, MTCY338.02c / Production host: ![]() ![]() ![]() References: UniProt: P9WI69, ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.65 Å3/Da / Density % sol: 73.56 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NaCl 4.3 M, 0.1 M Hepes-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.03→48.88 Å / Num. obs: 22374 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 96.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.03→3.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / CC1/2: 0.905 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 5M07 Resolution: 3.03→48.88 Å / Cor.coef. Fo:Fc: 0.9356 / Cor.coef. Fo:Fc free: 0.9189 / SU R Cruickshank DPI: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.258
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Displacement parameters | Biso mean: 87.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.374 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.03→48.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.03→3.18 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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