+Open data
-Basic information
Entry | Database: PDB / ID: 7u2r | ||||||
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Title | Structure of Paenibacillus sp. J14 Apyc1 | ||||||
Components | Apyc1 | ||||||
Keywords | HYDROLASE / Anti-Pycsar / Nuclease / Immune evasion | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase domain protein Function and homology information | ||||||
Biological species | Paenibacillus sp. J14 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 | 7u2r.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u2r.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 7u2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u2r_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 7u2r_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 7u2r_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 7u2r_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/7u2r ftp://data.pdbj.org/pub/pdb/validation_reports/u2/7u2r | HTTPS FTP |
-Related structure data
Related structure data | 7t26C 7t27C 7t28C 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: 27830.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. J14 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C6J7N0 | ||||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | The sequence conflict is due to strain variation. The correct sequence can be found in GB entry WP_ ...The sequence conflict is due to strain variation. The correct sequence can be found in GB entry WP_028539944.1. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tric-HCl pH 8.5, 0.2 M MgCl2, 16% 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: Feb 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→38.14 Å / Num. obs: 39926 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 33.15 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2401 / Rpim(I) all: 0.666 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→38.14 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1429 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: 45.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→38.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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