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Yorodumi- PDB-1jqw: THE 2.3 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jqw | ||||||
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Title | THE 2.3 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/HOMOCYSTEINE COMPLEX | ||||||
Components | Autoinducer-2 production protein luxS | ||||||
Keywords | SIGNALING PROTEIN / AUTOINDUCER SYNTHESIS | ||||||
Function / homology | Function and homology information S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / quorum sensing / iron ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
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. ...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. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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: Journal: TO BE PUBLISHED 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jqw.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jqw.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jqw_validation.pdf.gz | 392.5 KB | Display | wwPDB validaton report |
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Full document | 1jqw_full_validation.pdf.gz | 394.7 KB | Display | |
Data in XML | 1jqw_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1jqw_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jqw ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jqw | HTTPS FTP |
-Related structure data
Related structure data | 1j98SC 1jviC S: Starting model for refinement C: citing same article (ref.) |
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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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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.) Bacillus subtilis (bacteria) / Gene: luxS / Plasmid: pSKD1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) pLacI / References: UniProt: O34667, S-ribosylhomocysteine lyase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: 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: 2.28 Å3/Da / Density % sol: 46.05 % | |||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J98 Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.52 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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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
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