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Yorodumi- PDB-6g4j: Structure of the protein kinase YabT from Bacillus subtilis in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g4j | ||||||
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Title | Structure of the protein kinase YabT from Bacillus subtilis in complex with an alphaREP crystallization helper | ||||||
Components |
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Keywords | TRANSFERASE / Bacterial Hanks-type protein kinase / complex with an artificial binder / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information protein serine/threonine kinase activity => GO:0004674 / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å | ||||||
Authors | Nessler, S. / Cavagnino, A. / Rabefiraisana, J.L. | ||||||
Citation | Journal: Front Microbiol / Year: 2018 Title: Structural Analysis of the Hanks-Type Protein Kinase YabT FromBacillus subtilisProvides New Insights in its DNA-Dependent Activation. Authors: Shi, L. / Cavagnino, A. / Rabefiraisana, J.L. / Lazar, N. / Li de la Sierra-Gallay, I. / Ochsenbein, F. / Valerio-Lepiniec, M. / Urvoas, A. / Minard, P. / Mijakovic, I. / Nessler, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g4j.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g4j.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 6g4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g4j ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g4j | 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: 35023.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The C-terminal transmembrane helix of YabT (residues 316-338) has been deleted. The juxtamembrane region (residues 274-315) is disordered. Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: yabT, BSU00660 / Production host: Escherichia coli BL21(DE3) / Variant (production host): Rosetta References: UniProt: P37562, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 15864.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal His-tag and the C-terminal linker are disordered. Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: 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: 2.41 Å3/Da / Density % sol: 49.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 8000, Hepes, |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→50 Å / Num. all: 203500 / Num. obs: 56285 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rrim(I) all: 0.053 / Net I/σ(I): 14.11 |
Reflection shell | Resolution: 1.599→1.7 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 8958 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→40.513 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.28 Å2 / Biso mean: 32.7074 Å2 / Biso min: 15.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.599→40.513 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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