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Yorodumi- PDB-7mxk: Crystal structure of the S/T protein kinase PknG from Corynebacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mxk | ||||||
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Title | Crystal structure of the S/T protein kinase PknG from Corynebacterium glutamicum (residues 130-433) in complex with AMP-PNP, isoform 2 | ||||||
Components | Serine/threonine protein kinases | ||||||
Keywords | TRANSFERASE / metabolic control / glutamate metabolism / bacterial protein kinase / tetratricopeptide repeats | ||||||
Function / homology | Function and homology information phosphorylation / protein serine/threonine kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Lisa, M.N. / Alzari, P.M. | ||||||
Funding support | France, 1items
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Citation | Journal: Mbio / Year: 2021 Title: A Tetratricopeptide Repeat Scaffold Couples Signal Detection to OdhI Phosphorylation in Metabolic Control by the Protein Kinase PknG. Authors: Lisa, M.N. / Sogues, A. / Barilone, N. / Baumgart, M. / Gil, M. / Grana, M. / Duran, R. / Biondi, R.M. / Bellinzoni, M. / Bott, M. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mxk.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mxk.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 7mxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mxk_validation.pdf.gz | 744.4 KB | Display | wwPDB validaton report |
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Full document | 7mxk_full_validation.pdf.gz | 746 KB | Display | |
Data in XML | 7mxk_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7mxk_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/7mxk ftp://data.pdbj.org/pub/pdb/validation_reports/mx/7mxk | HTTPS FTP |
-Related structure data
Related structure data | 7mxbSC 7mxjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33272.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria) Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: Cgl2751 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NM29 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-MAP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 100 mM Tris-HCl, 27-30% w/v PEG 4 k, 200 mM MgCl2, pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→48.83 Å / Num. obs: 21235 / % possible obs: 98.4 % / Redundancy: 6 % / Biso Wilson estimate: 29.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.654 / Num. unique obs: 1207 / CC1/2: 0.751 / Rpim(I) all: 0.306 / Rrim(I) all: 0.725 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7MXB Resolution: 1.99→43.77 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3222 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→43.77 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.113720250801 Å / Origin y: 17.565592884 Å / Origin z: -18.6506305899 Å
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Refinement TLS group | Selection details: all |