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Yorodumi- PDB-1jvi: THE 2.2 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jvi | |||||||||
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Title | THE 2.2 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/RIBOSILHOMOCYSTEINE 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: 2.2 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: Acta Crystallogr.,Sect.D / Year: 2001 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. / Hartley, A. / Horsburg, 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 | 1jvi.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jvi.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jvi_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 1jvi_full_validation.pdf.gz | 472.7 KB | Display | |
Data in XML | 1jvi_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1jvi_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jvi ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jvi | HTTPS FTP |
-Related structure data
Related structure data | 1j98SC 1jqwC 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 second part of the biological assembly is generated by the two fold axis: X, X-Y, 5/6-Z |
-Components
-Protein / Sugars , 2 types, 2 molecules A
#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 |
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#4: Sugar | ChemComp-RHC / ( |
-Non-polymers , 4 types, 84 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-HCS / |
#6: 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: 2.55 Å3/Da / Density % sol: 45.3 % | |||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1.8 - 2.4M AMMONIUM SULPHATE, 0.1M TRIS-HCL, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||
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 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 8944 / Num. obs: 8944 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Biso Wilson estimate: 36.49 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.36 / Num. unique all: 553 / % possible all: 92.5 |
Reflection | *PLUS Num. measured all: 24877 |
Reflection shell | *PLUS Num. unique obs: 339 / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J98 Resolution: 2.2→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: 37.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 1 / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.142 |