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- PDB-6exl: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6exl | |||||||||
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Title | The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (MK206) - folded HTH motif | |||||||||
![]() | Listeriolysin positive regulatory factor A | |||||||||
![]() | DNA BINDING PROTEIN / Transcription regulator / DNA binding / 2-pyridone / drug design / Listeria monocytogenes | |||||||||
Function / homology | ![]() positive regulation of single-species biofilm formation on inanimate substrate / DNA-binding transcription factor activity / DNA binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hall, M. / Grundstrom, C. / Begum, A. / Kulen, M. / Lindgren, M. / Johansson, J. / Almqvist, F. / Sauer, U.H. / Sauer-Eriksson, A.E. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | 92.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6eutC ![]() 6euuC ![]() 6euzC ![]() 6ev0C ![]() 6exkC ![]() 6exmC ![]() 5f1rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27533.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Following cell lysis, the protein was extracted by Ni-NTA Superflow FF, followed by TEV protease cleavage in buffer (200 mM NaCl, 1 mM BME, 20 mM NaP (NaH2PO4+Na2HPO4, pH 7.1). Further ...Details: Following cell lysis, the protein was extracted by Ni-NTA Superflow FF, followed by TEV protease cleavage in buffer (200 mM NaCl, 1 mM BME, 20 mM NaP (NaH2PO4+Na2HPO4, pH 7.1). Further purification included Ni-NTA, MonoS and Gelfiltration (in 200 mM NaCl and 20 mM NaP buffer pH 6.5). Purified 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.897 Å / Num. obs: 38994 / % possible obs: 99.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F1R Resolution: 1.9→43.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.09 / 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: 1.9→43.9 Å
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Refine LS restraints |
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LS refinement shell |
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