[English] 日本語
![](img/lk-miru.gif)
- PDB-1jqw: THE 2.3 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/H... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jqw | ||||||
---|---|---|---|---|---|---|---|
Title | THE 2.3 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/HOMOCYSTEINE COMPLEX | ||||||
![]() | 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: 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 45.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 394.7 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j98SC ![]() 1jviC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the matrix: BIOMT1 2 0.500000 0.866025 0.000000 -31.39000 BIOMT2 2 0.866025 -0.500000 0.000000 54.36907 BIOMT3 2 0.000000 0.000000 -1.000000 -24.93000 |
-
Components
#1: Protein | Mass: 17790.219 Da / Num. of mol.: 1 / Mutation: P96T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 7264 / Num. obs: 7264 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.36 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.35 / Num. unique all: 494 / % possible all: 94.5 |
Reflection | *PLUS Num. measured all: 38530 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 94.5 % / Num. unique obs: 185 / Rmerge(I) obs: 0.501 |
-
Processing
Software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1J98 Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.52 Å2 | |||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| |||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 1 / Rfactor obs: 0.175 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|