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Open data
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Basic information
Entry | Database: PDB / ID: 1bdj | ||||||
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Title | COMPLEX STRUCTURE OF HPT DOMAIN AND CHEY | ||||||
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![]() | COMPLEX (CHEMOTAXIS/TRANSFERASE) / TWO-COMPONENT SYSTEM / HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAIN / ARCB / RESPONSE REGULATOR / CHEY / COMPLEX (CHEMOTAXIS-TRANSFERASE) / COMPLEX (CHEMOTAXIS-TRANSFERASE) complex | ||||||
Function / homology | ![]() peptidyl-histidine phosphorylation / 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 / response to oxygen levels / histidine phosphotransfer kinase activity / regulation of chemotaxis ...peptidyl-histidine phosphorylation / 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 / response to oxygen levels / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / histidine kinase / phosphorelay signal transduction system / plasma membrane => GO:0005886 / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / acetyltransferase activity / chemotaxis / protein autophosphorylation / regulation of DNA-templated transcription / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T. | ||||||
![]() | ![]() Title: Structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor protein ArcB complexed with the chemotaxis response regulator CheY. Authors: Kato, M. / Shimizu, T. / Mizuno, T. / Hakoshima, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.1 KB | Display | ![]() |
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PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 439.7 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13981.136 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE RESPONSE REGULATOR / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 14013.939 Da / Num. of mol.: 1 Fragment: HPT DOMAIN, THE HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P22763, UniProt: P0AEC3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 60 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Kato, M., (1998) Acta Crystallogr., D54, 140. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: COLLIMATER |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.68 Å / Num. obs: 9392 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 46.3 |
Reflection shell | Resolution: 2.68→3.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 84.2 |
Reflection | *PLUS Num. measured all: 40201 |
Reflection shell | *PLUS % possible obs: 75.8 % / Rmerge(I) obs: 0.405 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A0B (HPT DOMAIN) AND 1CHN (CHEY) Resolution: 2.68→10 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 41 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.68→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.8 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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