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Yorodumi- PDB-3lya: Crystal structure of the periplasmic domain of CadC in the presen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lya | ||||||
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Title | Crystal structure of the periplasmic domain of CadC in the presence of K2ReCl6 | ||||||
Components | Transcriptional activator cadC | ||||||
Keywords | SIGNALING PROTEIN / alpha/beta domain / alpha domain / Activator / DNA-binding / Transcription regulation / Two-component regulatory system | ||||||
Function / homology | Function and homology information phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Eichinger, A. / Skerra, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Crystal structure of the sensory domain of Escherichia coli CadC, a member of the ToxR-like protein family. Authors: Eichinger, A. / Haneburger, I. / Koller, C. / Jung, K. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lya.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lya.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/3lya ftp://data.pdbj.org/pub/pdb/validation_reports/ly/3lya | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41896.059 Da / Num. of mol.: 1 / Fragment: residues 188-512 Source method: isolated from a genetically manipulated source Details: The plasmid encodes a fusion protein comprising bacterial thioredoxin, a double His6-tag interspersed with a thrombin and an enterokinase cleavage site, and the CadC fragment comprising ...Details: The plasmid encodes a fusion protein comprising bacterial thioredoxin, a double His6-tag interspersed with a thrombin and an enterokinase cleavage site, and the CadC fragment comprising residues 188-512. Amino acid numbering of the crystal structure corresponds to the original numbering of the full length CadC protein sequence. Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MG1655 / Gene: b4133, cadC, JW4094 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) pLysS / References: UniProt: P23890 | ||
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#2: Chemical | ChemComp-RHE / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M ammonium sulfate, 6 % (v/v) 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.17652, 1.17705, 1.07813 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2008 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si-111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 14.1 % / Av σ(I) over netI: 6.2 / Number: 247813 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / D res high: 2.3 Å / D res low: 69.768 Å / Num. obs: 17592 / % possible obs: 99 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.3→69.77 Å / Num. all: 17592 / Num. obs: 17592 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rsym value: 0.095 / Net I/σ(I): 19.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 7.3 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→69.77 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.854 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.257 / SU ML: 0.157 / SU R Cruickshank DPI: 0.357 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.702 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→69.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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