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- PDB-8ju9: Molecular mechanism of the one-component regulator RccR on bacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ju9 | ||||||
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Title | Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence | ||||||
![]() | Probable transcriptional regulator | ||||||
![]() | DNA BINDING PROTEIN / One-component systems / KDPG-binding | ||||||
Function / homology | 2-KETO-DEOXY-GALACTOSE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rui, B. / Yibo, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence. Authors: Zhu, Y. / Mou, X. / Song, Y. / Zhang, Q. / Sun, B. / Liu, H. / Tang, H. / Bao, R. #1: ![]() Title: Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence Authors: Rui, B. / Yibo, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.8 KB | Display | ![]() |
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PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 30205.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-KDP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PG5 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris (pH 8.0), 8%PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.66 Å / Num. obs: 29112 / % possible obs: 98.97 % / Redundancy: 5.2 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 1 / Net I/σ(I): 25.28 |
Reflection shell | Resolution: 2→2.071 Å / Num. unique obs: 2760 / CC1/2: 0.858 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 45.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.66 Å
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Refine LS restraints |
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LS refinement shell |
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