+Open data
-Basic information
Entry | Database: PDB / ID: 6dsp | |||||||||
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Title | LsrB from Clostridium saccharobutylicum in complex with AI-2 | |||||||||
Components | Autoinducer 2-binding protein LsrB | |||||||||
Keywords | SIGNALING PROTEIN / AI-2 receptor | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium saccharobutylicum DSM 13864 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Torcato, I.M. / Xavier, K.B. / Miller, S.T. | |||||||||
Funding support | Portugal, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Identification of novel autoinducer-2 receptors inClostridiareveals plasticity in the binding site of the LsrB receptor family. Authors: Torcato, I.M. / Kasal, M.R. / Brito, P.H. / Miller, S.T. / Xavier, K.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dsp.cif.gz | 311.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dsp.ent.gz | 209.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dsp_validation.pdf.gz | 458.9 KB | Display | wwPDB validaton report |
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Full document | 6dsp_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 6dsp_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 6dsp_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/6dsp ftp://data.pdbj.org/pub/pdb/validation_reports/ds/6dsp | HTTPS FTP |
-Related structure data
Related structure data | 1tjyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37382.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium saccharobutylicum DSM 13864 (bacteria) Gene: lsrB, CLSA_c21430 / Plasmid: pDEST-527 / Production host: Escherichia coli (E. coli) / References: UniProt: U5MRH9 #2: Sugar | #3: 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: 2.52 Å3/Da / Density % sol: 51.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Citric acid pH 2.75 and 26% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→50.49 Å / Num. obs: 160886 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Χ2: 0.79 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7881 / CC1/2: 0.731 / Rpim(I) all: 0.509 / Rrim(I) all: 0.967 / Χ2: 0.61 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tjy Resolution: 1.37→50.49 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 19.77 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→50.49 Å
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LS refinement shell | Resolution: 1.37→1.49 Å
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