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- PDB-3a0y: Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a0y | ||||||
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Title | Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 3: 1,2-propanediol, orthorombic) | ||||||
![]() | Sensor protein | ||||||
![]() | TRANSFERASE / ATP-lid / 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 | ![]() | 77.9 KB | Display | ![]() |
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PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 435.9 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a0rC ![]() 3a0sC ![]() 3a0tC ![]() 3a0uC ![]() 3a0vC ![]() 3a0wSC ![]() 3a0xC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17726.236 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 25% 1,2-propanediol, 10% glycerol, 5% phosphate-citrate, 5% PEG3000, pH 4.5, 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: Mar 3, 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: 1.57→20 Å / Num. obs: 41793 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.04 / Net I/σ(I): 41.7 |
Reflection shell | Resolution: 1.57→1.64 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.444 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A0W Resolution: 1.57→19.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.596 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.095 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.71 Å2 / Biso mean: 20.002 Å2 / Biso min: 9.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.572→1.613 Å / Total num. of bins used: 20
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