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- PDB-4kl7: Crystal structure of the catalytic domain of RpfB from Mycobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kl7 | ||||||
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Title | Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis | ||||||
![]() | Resuscitation-promoting factor RpfB | ||||||
![]() | HYDROLASE / cell wall hydrolase | ||||||
Function / homology | ![]() dormancy exit of symbiont in host / positive regulation of growth rate / Hydrolases / quorum sensing / regulation of cell population proliferation / hydrolase activity / negative regulation of gene expression / positive regulation of gene expression / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Squeglia, F. / Romano, M. / Ruggiero, A. / Berisio, R. | ||||||
![]() | ![]() Title: Carbohydrate Recognition by RpfB from Mycobacterium tuberculosis Unveiled by Crystallographic and Molecular Dynamics Analyses. Authors: Squeglia, F. / Romano, M. / Ruggiero, A. / Vitagliano, L. / De Simone, A. / Berisio, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.8 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.7 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8534.348 Da / Num. of mol.: 4 / Fragment: UNP residues 283-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O05594, UniProt: P9WG29*PLUS, Hydrolases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 6 mg mL-1, 0,5% (w/v) PEG8000, 1M ammonium sulphate, 0,1 M Hepes, pH 7.5, and 120 mM benzamidine , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Saturn944 / Detector: CCD |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. all: 38135 / Num. obs: 38135 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.104 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→25.327 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.488 Å / Total num. of bins used: 20
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