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Yorodumi- PDB-4le1: Crystal structure of the receiver domain of DesR in the inactive state -
+Open data
-Basic information
Entry | Database: PDB / ID: 4le1 | ||||||
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Title | Crystal structure of the receiver domain of DesR in the inactive state | ||||||
Components | Transcriptional regulatory protein DesR | ||||||
Keywords | DNA BINDING PROTEIN / Response regulator / two-component system / transcription factor / receiver domain | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 Å | ||||||
Authors | Trajtenberg, F. / Larrieux, N. / Buschiazzo, A. | ||||||
Citation | Journal: MBio / Year: 2014 Title: Allosteric activation of bacterial response regulators: the role of the cognate histidine kinase beyond phosphorylation. Authors: Trajtenberg, F. / Albanesi, D. / Ruetalo, N. / Botti, H. / Mechaly, A.E. / Nieves, M. / Aguilar, P.S. / Cybulski, L. / Larrieux, N. / de Mendoza, D. / Buschiazzo, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4le1.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4le1.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 4le1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4le1_validation.pdf.gz | 458.1 KB | Display | wwPDB validaton report |
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Full document | 4le1_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 4le1_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4le1_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4le1 ftp://data.pdbj.org/pub/pdb/validation_reports/le/4le1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15108.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: desR, yocG, BSU19200 / Plasmid: pQE80L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10F' / References: UniProt: O34723 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-ACT / | #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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M (NH4)2SO4, 0.2 M NH4CH3CO2, vapor diffusion, hanging drop, temperature 291K, pH 8, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 9, 2011 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.951→62.106 Å / Num. all: 19564 / Num. obs: 19564 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 16.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→19.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9214 / Occupancy max: 1 / Occupancy min: 0.32 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 101.15 Å2 / Biso mean: 30.4806 Å2 / Biso min: 9.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.951→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.06 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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