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Yorodumi- PDB-8cb5: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cb5 | |||||||||
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Title | The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with tripeptide Glu-Val-Phe | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA BINDING PROTEIN / PRFA / LISTERIA INHIBITION / VIRULENCE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Listeria monocytogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Oelker, M. / Sauer-Eriksson, A.E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: To Be Published Title: Structural basis of promiscuous inhibition of virulence activator PrfA by nutritional peptides Authors: Oelker, M. / Lindgren, C. / Grundstrom, C. / Krypotou, E. / Scortti, M. / Hainzl, T. / Vazquez-Boland, J. / Sauer-Eriksson, A.E. #1: Journal: Cell Rep / Year: 2019 Title: Control of Bacterial Virulence through the Peptide Signature of the Habitat. Authors: Krypotou, E. / Scortti, M. / Grundstrom, C. / Oelker, M. / Luisi, B.F. / Sauer-Eriksson, A.E. / Vazquez-Boland, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cb5.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cb5.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 8cb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/8cb5 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/8cb5 | HTTPS FTP |
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-Related structure data
Related structure data | 8cb4C 8cb7C 8cb8C 8cbgC 8cbiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27457.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, lmo0200 / Production host: Escherichia coli (E. coli) / References: UniProt: P22262 #2: Protein/peptide | Mass: 393.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.13 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 3.1-6.6 mg mL-1, 20 mM NaP pH 6.5, 200 mM NaCl was mixed with peptides (0.5-2.5% DMSO, 1-4 mM DTT) in ratio 1:10. Well solution: 100 mM Nacitrate pH 5.1-5.7, 17% isopropanol, 16-26% ...Details: Protein: 3.1-6.6 mg mL-1, 20 mM NaP pH 6.5, 200 mM NaCl was mixed with peptides (0.5-2.5% DMSO, 1-4 mM DTT) in ratio 1:10. Well solution: 100 mM Nacitrate pH 5.1-5.7, 17% isopropanol, 16-26% PEG4000. Dropsize 1:1 microL Cryoprotection: 35% PEG4000 PH range: 5.1-5.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→47.33 Å / Num. obs: 23242 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.053 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2263 / CC1/2: 0.546 / Rpim(I) all: 0.59 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.33 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.64 Å2 / Biso mean: 69.4232 Å2 / Biso min: 33.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→47.33 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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