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Open data
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Basic information
Entry | Database: PDB / ID: 1zdm | ||||||
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Title | Crystal Structure of Activated CheY Bound to Xe | ||||||
![]() | Chemotaxis protein cheY | ||||||
![]() | SIGNALING PROTEIN / xenon binding / protein cavities / protein conformation assay / activated chey / response regulators / BeF3 | ||||||
Function / homology | ![]() bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / phosphorelay signal transduction system / phosphorelay sensor kinase activity / acetyltransferase activity / chemotaxis / magnesium ion binding / signal transduction / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lowery, T.J. / Doucleff, M. / Ruiz, E.J. / Rubin, S.M. / Pines, A. / Wemmer, D.E. | ||||||
![]() | ![]() Title: Distinguishing multiple chemotaxis Y protein conformations with laser-polarized 129Xe NMR. Authors: Lowery, T.J. / Doucleff, M. / Ruiz, E.J. / Rubin, S.M. / Pines, A. / Wemmer, D.E. #1: ![]() Title: Crystal structure of activated CheY. Comparison with other activated receiver domains. Authors: Lee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Berry, E.A. / Wemmer, D.E. #2: ![]() Title: NMR structure of activated chey Authors: Cho, H.S. / Lee, S.Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G. #3: ![]() Title: Crystal structure of an activated response regulator bound to its target. Authors: Lee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D.S. / Huang, L. / Kustu, S. / Berry, E.A. / Wemmer, D.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.6 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ny5S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14177.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 1.8 M ammonium sulfate, 5-10% glycerol, 100 mM Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2003 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→80.58 Å / Num. all: 19020 / Num. obs: 19018 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.103 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2801 / Rsym value: 0.439 / % possible all: 99.93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1NY5 amino acids 1-124 Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 52.3 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021
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