+Open data
-Basic information
Entry | Database: PDB / ID: 6p80 | ||||||
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Title | Structure of E. coli MS115-1 CdnC + ATP | ||||||
Components | E. coli MS115-1 NucC | ||||||
Keywords | PROTEIN BINDING / Second-messenger signaling / CD-NTase / cGAS | ||||||
Function / homology | Function and homology information 2'-5'-oligoadenylate synthetase activity / diadenylate cyclase activity / diadenylate cyclase / nucleotide metabolic process / double-stranded RNA binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli MS 115-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Ye, Q. / Azimi, C.S. / 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 | 6p80.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p80.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 6p80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p80_validation.pdf.gz | 758.4 KB | Display | wwPDB validaton report |
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Full document | 6p80_full_validation.pdf.gz | 761.7 KB | Display | |
Data in XML | 6p80_validation.xml.gz | 17 KB | Display | |
Data in CIF | 6p80_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/6p80 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p80 | HTTPS FTP |
-Related structure data
Related structure data | 6p82C 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 / Details: Native Data / Metadata reference: 10.15785/SBGRID/668 |
Experimental dataset #2 | Data set type: diffraction image data / Details: SeMet data / Metadata reference: 10.15785/SBGRID/669 |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36217.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli MS 115-1 (bacteria) / Gene: HMPREF9540_01758 / Production host: Escherichia coli (E. coli) / References: UniProt: D7Y2H2 |
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-Non-polymers , 5 types, 298 molecules
#2: Chemical | ChemComp-ATP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-MPD / ( |
#6: Water | ChemComp-HOH / |
-Details
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: 2.32 Å3/Da / Density % sol: 47.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 20 mM HEPES pH 8.1, 10-12% PEG 4000, 100 mM NaCl, 10 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 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: 1.44→19.23 Å / Num. obs: 60488 / % possible obs: 98.6 % / Redundancy: 3 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.019 / Rrim(I) all: 0.034 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.44→1.46 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.429 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2932 / CC1/2: 0.263 / Rpim(I) all: 1.04 / Rrim(I) all: 1.776 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→19.227 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.82 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.227 Å
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Refine LS restraints |
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LS refinement shell |
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