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- PDB-7e6g: Crystal structure of diguanylate cyclase SiaD in complex with its... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e6g | |||||||||
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Title | Crystal structure of diguanylate cyclase SiaD in complex with its activator SiaC from Pseudomonas aeruginosa | |||||||||
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![]() | DE NOVO PROTEIN / diguanylate cyclase / activation / Pseudomonas aeruginosa / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhou, J.S. / Zhang, L. / Zhang, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for diguanylate cyclase activation by its binding partner in Pseudomonas aeruginosa . Authors: Chen, G. / Zhou, J. / Zuo, Y. / Huo, W. / Peng, J. / Li, M. / Zhang, Y. / Wang, T. / Zhang, L. / Zhang, L. / Liang, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222 KB | Display | ![]() |
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PDB format | ![]() | 175.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 58.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i5aS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31587.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pleD_3, pleD_1, pleD_4, NCTC12951_03415, NCTC13437_04900, NCTC13621_04785, PAMH19_0165, RW109_RW109_00771 Production host: ![]() ![]() #2: Protein | Mass: 14655.237 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-G2P / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.01 M Spermidine trihydrochloride and 15% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 40897 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 0.982 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Num. unique obs: 4204 / CC1/2: 0.588 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3I5A Resolution: 2.65→46.295 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.71 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.86 Å2 / Biso mean: 55.2951 Å2 / Biso min: 11.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→46.295 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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