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Yorodumi- PDB-2n5t: Ensemble solution structure of the phosphoenolpyruvate-Enzyme I c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n5t | ||||||
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Title | Ensemble solution structure of the phosphoenolpyruvate-Enzyme I complex from the bacterial phosphotransferase system | ||||||
Components | Phosphoenolpyruvate-protein phosphotransferasePhosphoenolpyruvate—protein phosphotransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / SOLUTION SCATTERING / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Venditti, V. / Schwieters, C.D. / Grishaev, A. / Clore, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Authors: Venditti, V. / Schwieters, C.D. / Grishaev, A. / Clore, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n5t.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2n5t.ent.gz | 3.2 MB | Display | PDB format |
PDBx/mmJSON format | 2n5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/2n5t ftp://data.pdbj.org/pub/pdb/validation_reports/n5/2n5t | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 63635.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ptsI, b2416, JW2409 / Production host: Escherichia coli (E. coli) References: UniProt: P08839, phosphoenolpyruvate-protein phosphotransferase |
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-Experimental details
-Experiment
Experiment |
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NMR experiment |
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-Sample preparation
Details | Contents: 0.4 mM [U-13C; U-15N; U-2H] EIA, 20 mM TRIS, 1 mM EDTA, 100 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 310 K |
-Data collection
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 Details: The deposited structures represent two-membered ensembles with varying weights which must be considered together to properly reproduce the RDC and SAXS data. The first members of 10 ...Details: The deposited structures represent two-membered ensembles with varying weights which must be considered together to properly reproduce the RDC and SAXS data. The first members of 10 ensembles are reported in models 1-10 which were allowed rigid-body motion of subunits, arbitrary motion of linker regions and torsion degrees of freedom for sidechains. The second member of each ensemble is represented in model 11, which was fixed in the calculations. The ten pairs of weights for the ten ensemble members are Ensemble 1: MODEL 1, weight: 0.503 MODEL 11, weight: 0.497 Ensemble 2: MODEL 2, weight: 0.518 MODEL 11, weight: 0.482 Ensemble 3: MODEL 3, weight: 0.526 MODEL 11, weight: 0.474 Ensemble 4: MODEL 4, weight: 0.520 MODEL 11, weight: 0.480 Ensemble 5: MODEL 5, weight: 0.508 MODEL 11, weight: 0.492 Ensemble 6: MODEL 6, weight: 0.531 MODEL 11, weight: 0.469 Ensemble 7: MODEL 7, weight: 0.498 MODEL 11, weight: 0.501 Ensemble 8: MODEL 8, weight: 0.524 MODEL 11, weight: 0.476 Ensemble 9: MODEL 9, weight: 0.514 MODEL 11, weight: 0.486 Ensemble 10: MODEL 10, weight: 0.526 MODEL 11, weight: 0.474 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 11 / Maximum torsion angle constraint violation: 19.4 ° |