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- PDB-3a0z: 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: 3a0z | ||||||
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Title | Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 4: isopropanol, 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 | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 61.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.7 KB | Display | ![]() |
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Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a0rC ![]() 3a0sC ![]() 3a0tC ![]() 3a0uC ![]() 3a0vC ![]() 3a0wSC ![]() 3a0xC ![]() 3a0yC ![]() 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: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: 20% isopropanol, 0.1M sodium citrate, 20% PEG4000, pH 5.6, 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: 1.75→50 Å / Num. obs: 31968 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.044 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.245 / % possible all: 86.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A0W Resolution: 1.75→30.77 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.475 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.133 / 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: 57.32 Å2 / Biso mean: 20.355 Å2 / Biso min: 8.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.747→1.792 Å / Total num. of bins used: 20
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