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Yorodumi- PDB-5w43: Structure of the two-component response regulator RcsB-DNA complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w43 | ||||||
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Title | Structure of the two-component response regulator RcsB-DNA complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Rcs phosphorelay / response regulator / FixJ/NarL / Center for Structural Genomics of Infectious Diseases / CSGID / two-component signal transduction | ||||||
Function / homology | Function and homology information 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 | Escherichia coli str. K-12 substr. MG1655 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Filippova, E.V. / Warwzak, Z. / Pshenychnyi, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: MBio / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w43.cif.gz | 219.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w43.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 5w43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/5w43 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/5w43 | HTTPS FTP |
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-Related structure data
Related structure data | 5vxnC 1je8S 5i4cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
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.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Strain: K-12 substr. MG1655 / Gene: rcsB, b2217, JW2205 / Plasmid: pCA24n / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-magic / References: UniProt: P0DMC7 #2: DNA chain | | Mass: 6822.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: DNA chain | | Mass: 6675.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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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: 2.87 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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