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Yorodumi- PDB-5lrs: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lrs | |||||||||
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Title | The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with glutathione and a 30-bp operator PrfA-box motif | |||||||||
Components |
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Keywords | TRANSCRIPTION / Transcription regulator / DNA binding / activation / glutathione / Listeria monocytogenes | |||||||||
Function / homology | Function and homology information positive regulation of single-species biofilm formation on inanimate substrate / DNA-binding transcription factor activity / DNA binding / cytosol Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Hall, M. / Grundstrom, C. / Begum, A. / Lindberg, M. / Sauer, U.H. / Almqvist, F. / Johansson, J. / Sauer-Eriksson, A.E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria. Authors: Hall, M. / Grundstrom, C. / Begum, A. / Lindberg, M.J. / Sauer, U.H. / Almqvist, F. / Johansson, J. / Sauer-Eriksson, A.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lrs.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lrs.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lrs ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lrs | HTTPS FTP |
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-Related structure data
Related structure data | 5lejC 5lekC 5lrrC 2bgcS 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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-Components
#1: Protein | Mass: 27329.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, M643_11230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0, UniProt: P22262*PLUS #2: DNA chain | | Mass: 9261.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria) #3: DNA chain | | Mass: 9180.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria) #4: Chemical | #5: 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: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Prior to the crystallization setup GSH and DTT were added to the protein solution to final concentrations of 5 mM and 1 mM, respectively. Protein and duplex DNA were incubated together at a ...Details: Prior to the crystallization setup GSH and DTT were added to the protein solution to final concentrations of 5 mM and 1 mM, respectively. Protein and duplex DNA were incubated together at a ratio of 1:1.3 (PrfA dimer:hly DNA) at final concentrations of 50 microM and 70 microM respectively in 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM DTT for 60 min at room temperature, before being used for crystal setups. Crystals were obtained after 24 h by mixing 4 microL protein-DNA solution with 2 microL reservoir solution consisting of 8% PEG 8000, 100 mM sodium acetate pH 4.6, 100 mM magnesium acetate, 20% glycerol. Prior to vitrification the soaking of PrfAWT-DNA crystals were soaked in a reservoir solution containing 30% glycerol and 100 mM GSH for 24 h. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.073 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.073 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→58.9 Å / Num. obs: 19427 / % possible obs: 99.5 % / Redundancy: 25.6 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 26.2 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bgc Resolution: 2.9→54.636 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→54.636 Å
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Refine LS restraints |
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LS refinement shell |
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