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Yorodumi- PDB-7s54: Sortase A from Streptococcus agalactiae with the deltaN188 b7-b8 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s54 | ||||||
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Title | Sortase A from Streptococcus agalactiae with the deltaN188 b7-b8 loop sequence from Staphylococcus aureus Sortase A | ||||||
Components | Class A sortase, sortase A chimera | ||||||
Keywords | HYDROLASE / sortase-fold / sortase / eight-stranded beta barrel / transpeptidase / housekeeping sortase / surface protein | ||||||
Function / homology | Function and homology information sortase A / cysteine-type peptidase activity / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Streptococcus agalactiae (bacteria) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å | ||||||
Authors | Gao, M. / Kodama, H.M. / Antos, J.M. / Amacher, J.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes. Authors: Gao, M. / Johnson, D.A. / Piper, I.M. / Kodama, H.M. / Svendsen, J.E. / Tahti, E. / Longshore-Neate, F. / Vogel, B. / 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 | 7s54.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s54.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 7s54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s54_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 7s54_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 7s54_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 7s54_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/7s54 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/7s54 | HTTPS FTP |
-Related structure data
Related structure data | 7s53C 7s56C 7s57C 3rccS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 19027.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria), (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Gene: srtA, C4618_06055, F5043_06280, GD434_06060, NCTC6175_01342, RDF_0944, srtA, SAOUHSC_02834 Plasmid: pET28a(+) / Strain: NCTC 8325 / PS 47 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H1I052, UniProt: Q2FV99, sortase A #2: 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: 1.81 Å3/Da / Density % sol: 32.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.02 MES monohydrate pH 6, 12% (v/v) 2-Propanol, 24% (w/v) PEG monomethyl ether 2000 |
-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: Apr 14, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.79→35.631 Å / Num. obs: 25832 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RCC Resolution: 1.794→35.631 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.82 / 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: 67.6 Å2 / Biso mean: 25.8436 Å2 / Biso min: 8.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.794→35.631 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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