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Yorodumi- PDB-6euu: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6euu | |||||||||
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Title | The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (KSK29) | |||||||||
Components | Listeriolysin positive regulatory factor A | |||||||||
Keywords | DNA BINDING PROTEIN / Transcription regulator / DNA binding / 2-pyridone / drug design / 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: 2.6 Å | |||||||||
Authors | Begum, A. / Hall, M. / Grundstrom, C. / Kulen, M. / Lindgren, M. / Johansson, J. / Almqvist, F. / Sauer, U.H. / Sauer-Eriksson, A.E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes. Authors: Kulen, M. / Lindgren, M. / Hansen, S. / Cairns, A.G. / Grundstrom, C. / Begum, A. / van der Lingen, I. / Brannstrom, K. / Hall, M. / Sauer, U.H. / Johansson, J. / Sauer-Eriksson, A.E. / Almqvist, F. #1: Journal: Cell Chem Biol / Year: 2016 Title: Attenuating Listeria monocytogenes Virulence by Targeting the Regulatory Protein PrfA. Authors: Good, J.A. / Andersson, C. / Hansen, S. / Wall, J. / Krishnan, K.S. / Begum, A. / Grundstrom, C. / Niemiec, M.S. / Vaitkevicius, K. / Chorell, E. / Wittung-Stafshede, P. / Sauer, U.H. / ...Authors: Good, J.A. / Andersson, C. / Hansen, S. / Wall, J. / Krishnan, K.S. / Begum, A. / Grundstrom, C. / Niemiec, M.S. / Vaitkevicius, K. / Chorell, E. / Wittung-Stafshede, P. / Sauer, U.H. / Sauer-Eriksson, A.E. / Almqvist, F. / Johansson, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6euu.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6euu.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 6euu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/6euu ftp://data.pdbj.org/pub/pdb/validation_reports/eu/6euu | HTTPS FTP |
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-Related structure data
Related structure data | 6eutC 6euzC 6ev0C 6exkC 6exlC 6exmC 1f1rS C: citing same article (ref.) 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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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, AJN46_04535, BWI22_01025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0, UniProt: P22262*PLUS #2: Chemical | #3: Chemical | ChemComp-IPA / #4: Chemical | ChemComp-K29 / ( | #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: 2.26 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PrfA was co-crystallized with complex (5 mol excess) using the hanging-drop vapor-diffusion technique. Crystals grew in 5 days after 2 microL of the protein solution (3.2-3.5 mg per ml PrfA, ...Details: PrfA was co-crystallized with complex (5 mol excess) using the hanging-drop vapor-diffusion technique. Crystals grew in 5 days after 2 microL of the protein solution (3.2-3.5 mg per ml PrfA, 200 mM NaCl, 20 mM NaP buffer, pH 6.5) was mixed with an equal volume of precipitant solution containing 20-24% PEG-4000, 17% isopropanol, 100 mM Na citrate pH 5.5 and allowed to equilibrate over a 1 ml solution of the precipitant in a Linbro plate (Hampton Research). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.5 Å / Num. obs: 15110 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F1R Resolution: 2.6→45.5 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.96 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.5 Å
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Refine LS restraints |
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LS refinement shell |
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