+Open data
-Basic information
Entry | Database: PDB / ID: 6p82 | ||||||
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Title | Structure of P. aeruginosa ATCC27853 CdnD, Apo form 1 | ||||||
Components | Nucleotidyltransferase | ||||||
Keywords | SIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase | ||||||
Function / homology | Function and homology information diadenylate cyclase activity / diadenylate cyclase / nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Ye, Q. / Corbett, K.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2020 Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity. Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p82.cif.gz | 258.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p82.ent.gz | 217.7 KB | Display | PDB format |
PDBx/mmJSON format | 6p82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/6p82 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p82 | HTTPS FTP |
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-Related structure data
Related structure data | 6p80C 6p8jC 6p8oC 6p8pC 6p8rC 6p8sC 6p8uC 6p8vC 6pb3C 6u7bC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/670 |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34345.074 Da / Num. of mol.: 4 / Mutation: N-terminal SNA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: DY979_07585, EGY23_20895, IPC669_24880, PA5486_02902, PAERUG_E15_London_28_01_14_04351, PAMH19_6112 Production host: Escherichia coli (E. coli) / References: UniProt: A0A080VY32, UniProt: P0DTF7*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.32 Å3/Da / Density % sol: 62.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 1.8-2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→147.8 Å / Num. obs: 113653 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.058 / Rrim(I) all: 0.15 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.05→2.08 Å / Redundancy: 5.3 % / Rmerge(I) obs: 2.033 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5059 / CC1/2: 0.336 / Rpim(I) all: 0.906 / Rrim(I) all: 2.234 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→91.923 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 26.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→91.923 Å
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Refine LS restraints |
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LS refinement shell |
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