+Open data
-Basic information
Entry | Database: PDB / ID: 7l9c | ||||||
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Title | Receiver Domain of RssB | ||||||
Components | Regulator of RpoS | ||||||
Keywords | SIGNALING PROTEIN / receiver domain / response regulator / ClpXP adaptor | ||||||
Function / homology | Function and homology information sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / positive regulation of proteolysis / protein-DNA complex / protein destabilization / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Deaconescu, A.M. / Son, J. / Schwartz, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Phospho-dependent signaling during the general stress response by the atypical response regulator and ClpXP adaptor RssB. Authors: Schwartz, J. / Son, J. / Brugger, C. / Deaconescu, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l9c.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l9c.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 7l9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/7l9c ftp://data.pdbj.org/pub/pdb/validation_reports/l9/7l9c | HTTPS FTP |
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-Related structure data
Related structure data | 7lcmC 6od1S 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: 14566.069 Da / Num. of mol.: 1 / Fragment: Receiver Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MG1655 / Gene: rssB / Plasmid: pSKB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEV1 |
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#2: 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: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.2M lithium sulfate, 22% PEG 3,350, 0.1M Tris-HCl pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40.23 Å / Num. obs: 21241 / % possible obs: 98.91 % / Redundancy: 10.5 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.051 / Rsym value: 0.05 / Net I/σ(I): 24.77 |
Reflection shell | Resolution: 1.85→1.89 Å / Num. unique obs: 977 / CC1/2: 0.8 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OD1 Resolution: 1.85→37.1 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7159 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→37.1 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.9165202185 Å / Origin y: -10.9724718944 Å / Origin z: 9.4732087791 Å
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Refinement TLS group | Selection details: all |