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Yorodumi- PDB-5e1x: Crystal structure of the organohalide sensing RdhR-CbdbA1625 tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e1x | |||||||||
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Title | Crystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the 3,4-dichlorophenol bound form | |||||||||
Components | Transcriptional regulator, MarR familyTranscriptional regulation | |||||||||
Keywords | TRANSCRIPTION / MarR transcriptional regulator / DNA binding / organohalide binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Dehalococcoides mccartyi BTF08 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 Å | |||||||||
Authors | Quezada, C.P. / Dunstan, M.S. / Fisher, K. / Leys, D. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: TO BE PUBLISHED Title: Crystal structures of RdhRCbdbA1625 provide insight into sensing of chloroaromatic compounds by MarR-type regulators Authors: Quezada, C.P. / Dunstan, M.S. / Fisher, K. / Leys, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e1x.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e1x.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 5e1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e1x ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e1x | HTTPS FTP |
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-Related structure data
Related structure data | 5e1wSC 5e1zC 5e20C 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: 21016.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dehalococcoides mccartyi BTF08 (bacteria) Gene: rdhR, btf_1489 / Production host: Escherichia coli (E. coli) / References: UniProt: M1R817, UniProt: A0A1I9GEQ7*PLUS |
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#2: Chemical | ChemComp-5JD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Crystals formed in 0.1M Tris pH 7.5, 0.3M sodium acetate, 15% w/v PEG 4K were flash-cooled in liquid nitrogen by supplementing the mother liquor with 10% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.987 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→61.62 Å / Num. obs: 42515 / % possible obs: 99.87 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.46→1.69 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.074 / Mean I/σ(I) obs: 3.1 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5E1W Resolution: 1.46→61.62 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.958 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.537 Å2
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Refinement step | Cycle: 1 / Resolution: 1.46→61.62 Å
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Refine LS restraints |
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