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- PDB-7t8y: Structure of Class A sortase from Streptococcus pyogenes bound to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t8y | |||||||||
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Title | Structure of Class A sortase from Streptococcus pyogenes bound to lipid II mimetic, LPATA: Thr-in conformation | |||||||||
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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 | ![]() Synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Piper, I.M. / Antos, J.M. / Amacher, J.F. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Structures of Streptococcus pyogenes class A sortase in complex with substrate and product mimics provide key details of target recognition. Authors: Johnson, D.A. / Piper, I.M. / Vogel, B.A. / Jackson, S.N. / Svendsen, J.E. / Kodama, H.M. / Lee, D.E. / Lindblom, K.M. / McCarty, J. / 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 | ![]() | 54.3 KB | Display | ![]() |
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PDB format | ![]() | 35.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7s4oC ![]() 7s51C ![]() 7t8zC ![]() 3fn5S 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
#1: Protein | Mass: 18621.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: srtA_1, srtA, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY92_04850, GTK43_04765, GTK52_04270, GTK54_03910, GUA39_04435, IB935_04675, ...Gene: srtA_1, srtA, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY92_04850, GTK43_04765, GTK52_04270, GTK54_03910, GUA39_04435, IB935_04675, IB936_04605, IB937_04535, IB938_05195, KUN2590_09100, KUN4944_08330, SAMEA1407055_00305, SAMEA1711581_00311, SAMEA1711644_00960, SPNIH34_10200, SPNIH35_09070 Plasmid: pET18a(+) / Production host: ![]() ![]() |
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#2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 661.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) / References: BIRD: PRD_002489 |
#3: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 514.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) / References: BIRD: PRD_002489 |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 31.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.15 M Na acetate, 26% PEG 8000, 0.1 M Tris pH 6 |
-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: Oct 14, 2021 |
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: 1.8→45.103 Å / Num. obs: 25396 / % possible obs: 98.9 % / Redundancy: 5.87 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.999 / Rsym value: 0.074 / Net I/σ(I): 15.55 |
Reflection shell | Resolution: 1.8→1.91 Å / Mean I/σ(I) obs: 2.47 / Num. unique obs: 4137 / CC1/2: 0.84 / Rsym value: 0.53 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FN5 Resolution: 1.8→45.103 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.01 / Stereochemistry target values: ML
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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 max: 56.64 Å2 / Biso mean: 24.0546 Å2 / Biso min: 6.98 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→45.103 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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