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Yorodumi- PDB-3a0x: Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a0x | ||||||
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Title | Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 1: ammomium phosphate, monoclinic) | ||||||
Components | Sensor protein | ||||||
Keywords | TRANSFERASE / ATP-lid / Kinase / Phosphoprotein / Two-component regulatory system | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / regulation of DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y. | ||||||
Citation | Journal: Structure / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a0x.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a0x.ent.gz | 31.6 KB | Display | PDB format |
PDBx/mmJSON format | 3a0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/3a0x ftp://data.pdbj.org/pub/pdb/validation_reports/a0/3a0x | HTTPS FTP |
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-Related structure data
Related structure data | 3a0rC 3a0sC 3a0tC 3a0uC 3a0vC 3a0wSC 3a0yC 3a0zC 3a10C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17726.236 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1359 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q9X180, histidine kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.4M ammonium phosphate, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 5, 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: 1.89→50 Å / Num. obs: 10091 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.049 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.284 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A0W Resolution: 1.89→37.56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.531 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.211 / 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: 53.69 Å2 / Biso mean: 27.853 Å2 / Biso min: 14.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→37.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.889→1.938 Å / Total num. of bins used: 20
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