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Yorodumi- PDB-6qwf: The Transcriptional Regulator PrfA-A94V mutant from Listeria Mono... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qwf | ||||||
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Title | The Transcriptional Regulator PrfA-A94V mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / TRANSCRIPTION REGULATOR / ACTIVATION / LISTERIA MONOCYTOGENES / TRANSCRIPTION / VIRULENCE FACTOR | ||||||
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: 2.7 Å | ||||||
Authors | Hall, M. / Grundstrom, C. / Hansen, S. / Brannstrom, K. / Johansson, J. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Bacteriol. / Year: 2020 Title: A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes. Authors: Hansen, S. / Hall, M. / Grundstrom, C. / Brannstrom, K. / Sauer-Eriksson, A.E. / Johansson, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qwf.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qwf.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 6qwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qwf_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 6qwf_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 6qwf_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 6qwf_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/6qwf ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qwf | HTTPS FTP |
-Related structure data
Related structure data | 6qvyC 6qvzC 6qw1C 6qw2C 6qwhC 6qwkC 6qwmC 5lejS 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: 27485.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, CDR86_15285, D3B95_15085, DOE67_09655 / 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: 2.78 Å3/Da / Density % sol: 55.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Droplets of 4 microl protein-DNA solution (ratio 1:1.3) in 20 mM Tris-HCl pH 8.0, 50 mM NaCl, and 1 mM EDTA at 6 mg per ml were mixed with 2 microl reservoir solution consisting of 8% PEG ...Details: Droplets of 4 microl protein-DNA solution (ratio 1:1.3) in 20 mM Tris-HCl pH 8.0, 50 mM NaCl, and 1 mM EDTA at 6 mg per ml were mixed with 2 microl reservoir solution consisting of 8% PEG 8000, 100 mM sodium citrate pH 4.6, 100 mM Magnesium acetate and 20% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→42.56 Å / Num. obs: 23582 / % possible obs: 99.9 % / Redundancy: 26.8 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.026 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 28.3 % / Rmerge(I) obs: 1.367 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2304 / Rpim(I) all: 0.363 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LEJ Resolution: 2.7→42.557 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→42.557 Å
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Refine LS restraints |
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LS refinement shell |
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