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Open data
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Basic information
Entry | Database: PDB / ID: 3a0s | ||||||
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Title | PAS domain of histidine kinase ThkA (TM1359) | ||||||
![]() | Sensor protein | ||||||
![]() | TRANSFERASE / PAS-fold / Kinase / Phosphoprotein / Two-component regulatory system | ||||||
Function / homology | ![]() histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / regulation of DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y. | ||||||
![]() | ![]() Title: Structure of PAS-linked histidine kinase and the response regulator complex Authors: Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.1 KB | Display | ![]() |
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PDB format | ![]() | 25 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 457.7 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a0rC ![]() 3a0tC ![]() 3a0uC ![]() 3a0vSC ![]() 3a0wC ![]() 3a0xC ![]() 3a0yC ![]() 3a0zC ![]() 3a10C C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 11219.812 Da / Num. of mol.: 1 / Fragment: PAS domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-PG4 / #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 50% PEG200, 0.1M sodium/potassium-phosphate pH 6.2, 0.2M sodium chloride, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2007 |
Radiation | Monochromator: Si 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→30 Å / Num. obs: 19750 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 18.2 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.047 / Net I/σ(I): 41.5 |
Reflection shell | Resolution: 1.47→1.52 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.334 / % possible all: 88.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A0V Resolution: 1.47→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.51 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.41 Å2 / Biso mean: 27.384 Å2 / Biso min: 11.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 8.758 Å / Origin y: 5.128 Å / Origin z: 42.929 Å
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