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Open data
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Basic information
Entry | Database: PDB / ID: 1j98 | ||||||
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Title | The 1.2 Angstrom Structure of Bacillus subtilis LuxS | ||||||
![]() | AUTOINDUCER-2 PRODUCTION PROTEIN LUXS | ||||||
![]() | SIGNALING PROTEIN / Autoinducer synthesis | ||||||
Function / homology | ![]() S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / quorum sensing / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Hartley, A. / Foster, S.J. / Horsburgh, M.J. / Cox, A.G. / McCleod, C.W. / Mekhalfia, A. / Blackburn, G.M. ...Ruzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Hartley, A. / Foster, S.J. / Horsburgh, M.J. / Cox, A.G. / McCleod, C.W. / Mekhalfia, A. / Blackburn, G.M. / Rice, D.W. / Baker, P.J. | ||||||
![]() | ![]() Title: The 1.2 A Structure of a Novel Quorum-Sensing Protein, Bacillus subtilis LuxS Authors: Ruzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Hartley, A. / Foster, S.J. / Horsburgh, M.J. / Cox, A.G. / McCleod, C.W. / Mekhalfia, A. / Blackburn, G.M. / Rice, D.W. / Baker, P.J. #1: ![]() Title: Cloning, Purification, Crystallization and Preliminary Crystallographic Analysis of Bacillus subtilis LuxS Authors: Das, S.K. / Sedelnikova, S.E. / Baker, P.J. / Ruzheinikov, S.N. / Foster, S.J. / Hartley, A. / Horsburgh, M.J. / Rice, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.2 KB | Display | ![]() |
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PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.4 KB | Display | ![]() |
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Full document | ![]() | 370.4 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: x, x-y, 5/6-z. |
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Components
#1: Protein | Mass: 17790.219 Da / Num. of mol.: 1 / Mutation: P96T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 39.56 % | |||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8 - 2.4M Ammonium sulphate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→10 Å / Num. all: 53328 / Num. obs: 53328 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1714 / % possible all: 63.3 |
Reflection | *PLUS Num. measured all: 288300 |
Reflection shell | *PLUS % possible obs: 63.6 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 16.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.2 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.126 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.8 Å2 |