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- PDB-5w43: Structure of the two-component response regulator RcsB-DNA complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w43 | ||||||
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Title | Structure of the two-component response regulator RcsB-DNA complex | ||||||
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![]() | DNA BINDING PROTEIN / Rcs phosphorelay / response regulator / FixJ/NarL / Center for Structural Genomics of Infectious Diseases / CSGID / two-component signal transduction | ||||||
Function / homology | ![]() regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / positive regulation of cell projection organization / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex ...regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / positive regulation of cell projection organization / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Filippova, E.V. / Warwzak, Z. / Pshenychnyi, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB. Authors: Filippova, E.V. / Zemaitaitis, B. / Aung, T. / Wolfe, A.J. / Anderson, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.3 KB | Display | ![]() |
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PDB format | ![]() | 174.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 445.9 KB | Display | ![]() |
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Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vxnC ![]() 1je8S ![]() 5i4cS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 23699.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K-12 substr. MG1655 / Gene: rcsB, b2217, JW2205 / Plasmid: pCA24n / Production host: ![]() ![]() #2: DNA chain | | Mass: 6822.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: DNA chain | | Mass: 6675.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.19 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, 0.2 M ammonuim acetate, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 11, 2017 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→30 Å / Num. obs: 11611 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.7 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 3.15→3.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 5I4C & 1JE8 Resolution: 3.15→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 63.236 / SU ML: 0.468 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 121.88 Å2
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Refinement step | Cycle: 1 / Resolution: 3.15→30 Å
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Refine LS restraints |
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