+Open data
-Basic information
Entry | Database: PDB / ID: 5hwt | ||||||
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Title | Crystal structure of apo-PAS1 | ||||||
Components | Sensor histidine kinase TodS | ||||||
Keywords | TRANSFERASE / PAS / Two-component signal transduction / toluene | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Hwang, J. / Koh, S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2016 Title: Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System. Authors: Koh, S. / Hwang, J. / Guchhait, K. / Lee, E.G. / Kim, S.Y. / Kim, S. / Lee, S. / Chung, J.M. / Jung, H.S. / Lee, S.J. / Ryu, C.M. / Lee, S.G. / Oh, T.K. / Kwon, O. / Kim, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hwt.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hwt.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hwt ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hwt | HTTPS FTP |
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-Related 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: 14447.225 Da / Num. of mol.: 2 / Fragment: PAS1 (UNP RESIDUES 43-168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain F1 / ATCC 700007) (bacteria) Strain: F1 / ATCC 700007 / Gene: todS, Pput_2872 / Production host: Escherichia coli (E. coli) / References: UniProt: A5W4E3, histidine kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.39 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 3.0M ammonium phosphate, 0.1M Tris-HCl / PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 23475 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 32.94 |
Reflection shell | Resolution: 1.7→1.73 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.112 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.121
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.32 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→25 Å
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Refine LS restraints |
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