+Open data
-Basic information
Entry | Database: PDB / ID: 7s56 | ||||||
---|---|---|---|---|---|---|---|
Title | Sortase A from Streptococcus agalactiae, residues 79-247 | ||||||
Components | Class A sortase | ||||||
Keywords | HYDROLASE / sortase-fold / sortase / eight-standed beta barrel / transpeptidase / housekeeping sortase / surface protein | ||||||
Function / homology | Sortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Class A sortase Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Gao, M. / Kodama, H.M. / Antos, J.M. / Amacher, J.F. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7s56.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7s56.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 7s56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/7s56 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/7s56 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7s53C 7s54C 7s57C 3rccS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18417.990 Da / Num. of mol.: 1 / Fragment: UNP residues 79-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) Gene: srtA, C4618_06055, F5043_06280, GD434_06060, NCTC6175_01342, RDF_0944 Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H1I052 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.63 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 20% (v/v) 2-Propanol, 0.1 M MES monohydrate pH 6.1, 20% (w/v) PEG monomethyl ether 2000 |
-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: Apr 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: 1.4→40.47 Å / Num. obs: 29340 / % possible obs: 99.58 % / Redundancy: 12 % / Biso Wilson estimate: 14.58 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Rsym value: 0.05 / Net I/σ(I): 29.08 |
Reflection shell | Resolution: 1.42→1.5 Å / Mean I/σ(I) obs: 3.78 / Num. unique obs: 4598 / CC1/2: 0.953 / Rrim(I) all: 0.727 / Rsym value: 0.694 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RCC Resolution: 1.4→40.47 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.27 / 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: 46.62 Å2 / Biso mean: 17.5254 Å2 / Biso min: 8.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→40.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|