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- PDB-7kki: Crystal structure of the MarR family transcriptional regulator fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kki | ||||||
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Title | Crystal structure of the MarR family transcriptional regulator from Variovorax paradoxus bound to 2,4-Dichlorophenoxyacetic acid | ||||||
![]() | Transcriptional regulator, MarR family | ||||||
![]() | DNA BINDING PROTEIN / Transcriptional Regulator / Ligand Binding | ||||||
Function / homology | ![]() response to stress / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walton, W.G. / Redinbo, M.R. / Dangl, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Authors: Conway, J.M. / Walton, W.G. / Salas-Gonzalez, I. / Law, T.F. / Lindberg, C.A. / Crook, L.E. / Kosina, S.M. / Fitzpatrick, C.R. / Lietzan, A.D. / Northen, T.R. / Jones, C.D. / Finkel, O.M. / ...Authors: Conway, J.M. / Walton, W.G. / Salas-Gonzalez, I. / Law, T.F. / Lindberg, C.A. / Crook, L.E. / Kosina, S.M. / Fitzpatrick, C.R. / Lietzan, A.D. / Northen, T.R. / Jones, C.D. / Finkel, O.M. / Redinbo, M.R. / Dangl, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.6 KB | Display | ![]() |
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PDB format | ![]() | 33.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 456.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kfoSC ![]() 7kfqC ![]() 7kfsC ![]() 7kh3C ![]() 7kigC ![]() 7kjlC ![]() 7kjqC ![]() 7kk0C ![]() 7kkcC ![]() 7krhC ![]() 7kuaC ![]() 7kymC ![]() 7l19C ![]() 7l1iC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18225.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CFA / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Chloride, 0.1 M Bis-Tris: HCl, pH 6.5, 1.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45.32 Å / Num. obs: 24310 / % possible obs: 99.82 % / Redundancy: 2 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 1 / Net I/σ(I): 18.92 |
Reflection shell | Resolution: 1.6→1.657 Å / Num. unique obs: 2385 / CC1/2: 0.802 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7KFO Resolution: 1.6→40.96 Å / SU ML: 0.1803 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4395 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 31.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40.96 Å
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Refine LS restraints |
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LS refinement shell |
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