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- PDB-7cg9: Crystal structure of pilin-specific sortase SrtC1 from Lactobacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cg9 | ||||||
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Title | Crystal structure of pilin-specific sortase SrtC1 from Lactobacillus rhamnosus GG | ||||||
![]() | Class C sortase | ||||||
![]() | HYDROLASE / Pilin-specific sortase / cysteine-transpeptidase / pilus assembly / lactobacillar pilus / SpaCBA pilus / probiotics | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Megta, A.K. / Pratap, S. / Krishnan, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of pilin-specific sortase SrtC1 from Lactobacillus rhamnosus GG Authors: Megta, A.K. / Pratap, S. / Krishnan, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.6 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g1hS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27253.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A5P5ZBR6 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.94 % / Description: Three-dimensional diamond-shaped crystals |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M Lithium sulfate, 0.1 M Tris-Cl pH 8.0, 30% (w/v) PEG 4000 |
-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: Feb 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→42.32 Å / Num. obs: 12848 / % possible obs: 91 % / Redundancy: 21.9 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1400 / CC1/2: 0.81 / Rpim(I) all: 0.29 / Rrim(I) all: 0.89 / Χ2: 0.81 / % possible all: 70.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G1H Resolution: 2.05→42.32 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.765 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→42.32 Å
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Refine LS restraints |
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