[English] 日本語
Yorodumi- PDB-7t8z: Structure of Class A sortase from Streptococcus pyogenes bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t8z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Class A sortase from Streptococcus pyogenes bound to lipid II mimetic, LPATA: Thr-out conformation | |||||||||
Components |
| |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Streptococcus pyogenes (bacteria) Synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Piper, I.M. / Antos, J.M. / Amacher, J.F. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7t8z.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7t8z.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 7t8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/7t8z ftp://data.pdbj.org/pub/pdb/validation_reports/t8/7t8z | HTTPS FTP |
---|
-Related structure data
Related structure data | 7s4oC 7s51C 7t8yC 3fn5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18621.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) 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: pET28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U7I1I9 |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 31.15 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.15 M sodium acetate, 26% (w/v) PEG 8000, 0.1 M Tris pH 6 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS3 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: 1.9→44.881 Å / Num. obs: 21335 / % possible obs: 98.7 % / Redundancy: 6.98 % / Biso Wilson estimate: 22.82 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Rsym value: 0.083 / Net I/σ(I): 0.09 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 6.53 % / Mean I/σ(I) obs: 3.49 / Num. unique obs: 3401 / CC1/2: 0.85 / Rrim(I) all: 0.594 / Rsym value: 0.547 / % possible all: 97.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FN5 Resolution: 1.9→44.881 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.67 Å2 / Biso mean: 27.0534 Å2 / Biso min: 11.73 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→44.881 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|