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- PDB-8t8g: C208A Streptococcus pyogenes Sortase A (spySrtA) bound to LPALA p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t8g | ||||||
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Title | C208A Streptococcus pyogenes Sortase A (spySrtA) bound to LPALA peptide | ||||||
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![]() | HYDROLASE / SORTASE-FOLD / SORTASE / EIGHT-STRANDED BETA BARREL / TRANSPEPTIDASE / HOUSEKEEPING SORTASE / SURFACE PROTEIN | ||||||
Function / homology | Sortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Sortase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kodama, H.M. / Amacher, J.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A unique binding mode of P1' Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage. Authors: Vogel, B.A. / Blount, J.M. / Kodama, H.M. / Goodwin-Rice, N.J. / Andaluz, D.J. / Jackson, S.N. / Antos, J.M. / Amacher, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.9 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.4 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Unit cell |
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Components
#1: Protein | Mass: 18589.051 Da / Num. of mol.: 1 / Mutation: C208A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: srtA, srtA_1, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, ...Gene: srtA, srtA_1, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, GUA39_04435, IB935_04675, IB936_04605, IB937_04535, IB938_05195, KUN2590_09100, KUN4944_08330, MGAS2221_0893, SAMEA1407055_00305, SAMEA1711644_00960, SAMEA3918953_00457, SPNIH34_10200, SPNIH35_09070 Plasmid: pET28a(+) / Cell (production host): BL21 (DE3) / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 540.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Tris, 30% PEG 8000, 0.25 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2023 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35.66 Å / Num. obs: 43124 / % possible obs: 99.3 % / Redundancy: 6.28 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 1 / Rsym value: 0.034 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.27 / Num. unique obs: 6735 / CC1/2: 0.928 / Rsym value: 0.355 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→35.66 Å
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Refine LS restraints |
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LS refinement shell |
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