+Open data
-Basic information
Entry | Database: PDB / ID: 7t28 | ||||||
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Title | Structure of phage Bsp38 anti-Pycsar nuclease Apyc1 in apo state | ||||||
Components | Putative metal-dependent hydrolase | ||||||
Keywords | VIRAL PROTEIN / Anti-Pycsar / Nuclease / Immune evasion | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / hydrolase activity / Putative metal-dependent hydrolase Function and homology information | ||||||
Biological species | Bacillus phage BSP38 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Hobbs, S.J. / Wein, T. / Lu, A. / Morehouse, B.R. / Schnabel, J. / Sorek, R. / Kranzusch, P.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2022 Title: Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity. Authors: Hobbs, S.J. / Wein, T. / Lu, A. / Morehouse, B.R. / Schnabel, J. / Leavitt, A. / Yirmiya, E. / Sorek, R. / Kranzusch, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t28.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t28.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 7t28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/7t28 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/7t28 | HTTPS FTP |
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-Related structure data
Related structure data | 7t26C 7t27C 7u2rC 7u2sC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29169.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage BSP38 (virus) / Gene: BSP38_126 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A345MJY6 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 7.5, 30% PEG-4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→38.42 Å / Num. obs: 8581 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 76.17 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.071 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.7→2.83 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1129 / CC1/2: 0.883 / Rpim(I) all: 0.732 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold2 Resolution: 2.68→36.26 Å / SU ML: 0.5493 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.5205 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 107.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→36.26 Å
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Refine LS restraints |
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LS refinement shell |
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