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Yorodumi- PDB-7s4o: Structure of C208A Sortase A from Streptococcus pyogenes bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s4o | ||||||
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Title | Structure of C208A Sortase A from Streptococcus pyogenes bound to LPATS peptide | ||||||
Components |
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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: 1.396 Å | ||||||
Authors | Johnson, D.A. / Svendsen, J.E. / Antos, J.M. / Amacher, J.F. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s4o.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s4o.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 7s4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/7s4o ftp://data.pdbj.org/pub/pdb/validation_reports/s4/7s4o | HTTPS FTP |
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-Related structure data
Related structure data | 7s51C 7t8yC 7t8zC 3fn5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18589.051 Da / Num. of mol.: 2 / Mutation: C208A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) 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(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4U7I1I9 #2: Protein/peptide | Mass: 880.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% (w/v) PEG 8000, 0.1 M sodium acetate, 0.1 M Tris pH 6 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 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: 1.396→43.18 Å / Num. obs: 55913 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.01 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FN5 Resolution: 1.396→43.177 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.5 / 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: 54.17 Å2 / Biso mean: 14.5678 Å2 / Biso min: 4.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.396→43.177 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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