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Yorodumi- PDB-7kfs: Crystal structure of the MarR family transcriptional regulator fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kfs | ||||||
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Title | Crystal structure of the MarR family transcriptional regulator from Variovorax paradoxus bound to Benzoic Acid | ||||||
Components | Transcriptional regulator, MarR family | ||||||
Keywords | DNA BINDING PROTEIN / Transcriptional Regulator / Ligand Binding | ||||||
Function / homology | Function and homology information response to stress / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | Variovorax paradoxus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Walton, W.G. / Redinbo, M.R. / Dangl, J.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Microbiol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kfs.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kfs.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/7kfs ftp://data.pdbj.org/pub/pdb/validation_reports/kf/7kfs | HTTPS FTP |
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-Related structure data
Related structure data | 7kfoSC 7kfqC 7kh3C 7kigC 7kjlC 7kjqC 7kk0C 7kkcC 7kkiC 7krhC 7kuaC 7kymC 7l19C 7l1iC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20969.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1489 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP2 | ||||
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#2: Chemical | ChemComp-BEZ / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium Sulfate, 0.1 M HEPES: NaOH, pH 7.5, 25 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 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: 1.5→45.44 Å / Num. obs: 28967 / % possible obs: 99.87 % / Redundancy: 2 % / Biso Wilson estimate: 22.78 Å2 / CC1/2: 1 / Net I/σ(I): 17.88 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 2850 / CC1/2: 0.773 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KFO Resolution: 1.5→40.42 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6618 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: 30.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40.42 Å
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Refine LS restraints |
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LS refinement shell |
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