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- PDB-8gr6: Crystal Structure of pilus-specific Sortase C from Streptococcus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gr6 | ||||||
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Title | Crystal Structure of pilus-specific Sortase C from Streptococcus sanguinis | ||||||
![]() | Sortase-like protein, putative | ||||||
![]() | HYDROLASE / Sortase C / Pilus specific sortase / Cysteine-transpeptidase / Streptococcus sanguinis / dental plaque / biofilm | ||||||
Function / homology | Sortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / Sortase-like protein, putative![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yadav, S. / Parijat, P. / Krishnan, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the pilus-specific sortase from early colonizing oral Streptococcus sanguinis captures an active open-lid conformation. Authors: Yadav, S. / Parijat, P. / 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 | ![]() | 100.3 KB | Display | ![]() |
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PDB format | ![]() | 74 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.1 KB | Display | ![]() |
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Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8guuC ![]() 4d7wS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 24005.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SK36 / Gene: srtC, SSA_1631 / Variant: No / Plasmid: pET28b / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69 % / Description: Rhombohedral |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM Sodium acetate (pH 5.5), 200mM Ammonium-Sulphate and 10% (w/v) PEG 2000 MME and 12.5 mM Zinc-Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 2.056→52.331 Å / Num. obs: 23670 / % possible obs: 97.2 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.056→2.092 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1220 / CC1/2: 0.91 / Rpim(I) all: 0.23 / Rrim(I) all: 0.625 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D7W Resolution: 2.06→52.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 7.232 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.162 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→52.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.11 Å
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Refinement TLS params. | Method: refined / Origin x: 14.694 Å / Origin y: -15.999 Å / Origin z: -16.597 Å
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