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Yorodumi- PDB-6vu0: CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF ENZYME I OF THE BAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vu0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF ENZYME I OF THE BACTERIAL PHOSPHOTRANSFERASE SYSTEM FROM THE ESCHERICHIA COLI ENZYME | ||||||
Components | PEP-protein phosphotransferase system enzyme I | ||||||
Keywords | TRANSFERASE / phosphoenolpyruvate-protein phosphotransferase PtsI / enzyme I | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Stewart Jr., C.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Hybrid Thermophilic/Mesophilic Enzymes Reveal a Role for Conformational Disorder in Regulation of Bacterial Enzyme I. Authors: Dotas, R.R. / Nguyen, T.T. / Stewart Jr., C.E. / Ghirlando, R. / Potoyan, D.A. / Venditti, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vu0.cif.gz | 291.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vu0.ent.gz | 194.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/6vu0 ftp://data.pdbj.org/pub/pdb/validation_reports/vu/6vu0 | HTTPS FTP |
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-Related structure data
Related structure data | 6v9kSC 6vbjC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 261 - 569 / Label seq-ID: 2 - 310
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-Components
#1: Protein | Mass: 35350.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsI_2, NCTC9962_06426 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1V2SSS1, UniProt: P08839*PLUS, phosphoenolpyruvate-protein phosphotransferase #2: Chemical | Has ligand of interest | Y | |
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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: 6.04 Å3/Da / Density % sol: 79.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 500 mM Ammonium sulfate, 1.00 M Lithium sulfate, 100 mM tri-Sodium citrate pH 5.6, 1.0 mM TEW |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2019 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→37.07 Å / Num. obs: 54988 / % possible obs: 91.1 % / Redundancy: 5.2 % / Biso Wilson estimate: 94.51 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.164 / Rrim(I) all: 0.483 / Net I/σ(I): 3 / Num. measured all: 285184 / Scaling rejects: 803 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6V9K Resolution: 3.5→37.07 Å / SU ML: 0.5006 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.5409 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: 109.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→37.07 Å
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Refine LS restraints |
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LS refinement shell |
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