+Open data
-Basic information
Entry | Database: PDB / ID: 1kkm | ||||||
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Title | L.casei HprK/P in complex with B.subtilis P-Ser-HPr | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/TRANSPORT PROTEIN / phosphorylation / protein kinase / bacteria / protein/protein interaction / phosphoserine / HYDROLASE-TRANSPORT PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information regulation of carbohydrate utilization / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / regulation of carbohydrate metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate-dependent sugar phosphotransferase system / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / carbohydrate metabolic process / protein serine/threonine kinase activity / magnesium ion binding ...regulation of carbohydrate utilization / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / regulation of carbohydrate metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate-dependent sugar phosphotransferase system / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / carbohydrate metabolic process / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactobacillus casei (bacteria) Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fieulaine, S. / Morera, S. / Poncet, S. / Galinier, A. / Janin, J. / Deutscher, J. / Nessler, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr. Authors: Fieulaine, S. / Morera, S. / Poncet, S. / Mijakovic, I. / Galinier, A. / Janin, J. / Deutscher, J. / Nessler, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kkm.cif.gz | 165.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kkm.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 1kkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kkm ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kkm | HTTPS FTP |
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-Related structure data
Related structure data | 1kklC 1jb1S 1sphS C: citing same article (ref.) S: Starting model for refinement |
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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: 22679.652 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: PTSK / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): NM522 References: UniProt: Q9RE09, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Protein | Mass: 10783.985 Da / Num. of mol.: 3 / Mutation: G85R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PTSH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): NM522 / References: UniProt: P08877 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG-400, Hepes, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2001 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 23597 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2339 / Rsym value: 0.146 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 274803 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.146 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JB1 and 1SPH Resolution: 2.8→30 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.43 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.84 Å / Rfactor Rfree: 0.4 / Rfactor Rwork: 0.352 | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.257 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.4 / Rfactor Rwork: 0.352 |