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Open data
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Basic information
Entry | Database: PDB / ID: 6u7b | ||||||
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Title | Structure of E. coli MS115-1 CdnC:HORMA-deltaN complex | ||||||
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![]() | SIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase / HORMA domain / closure motif | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, Q. / Corbett, K.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 699.8 KB | Display | ![]() |
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PDB format | ![]() | 484.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.5 KB | Display | ![]() |
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Full document | ![]() | 805.9 KB | Display | |
Data in XML | ![]() | 38.7 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p80SC ![]() 6p82C ![]() 6p8jC ![]() 6p8oC ![]() 6p8pC ![]() 6p8rC ![]() 6p8sC ![]() 6p8uC ![]() 6p8vC ![]() 6pb3C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/711 |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 36217.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 20148.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 393 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-AMP / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M CHES pH 9.5, 0.1 M magnesium acetate, and 17% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→151.16 Å / Num. obs: 67360 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.305 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4202 / CC1/2: 0.566 / Rpim(I) all: 0.537 / Rrim(I) all: 1.414 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6P80 Resolution: 2.09→103.84 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.6294 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: 57.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→103.84 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 |
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