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Open data
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Basic information
Entry | Database: PDB / ID: 7l8n | |||||||||
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Title | Diadenylate cyclase with AMP from Streptococcus mutans | |||||||||
![]() | Diadenylate cyclase | |||||||||
![]() | TRANSFERASE / cyclase / ATP / AMP / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() : / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / nucleotidyltransferase activity / membrane => GO:0016020 / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hua, Z. / Hui, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Diadenylate cyclase with AMP from Streptococcus mutans Authors: Hua, Z. / Hui, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.8 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.8 KB | Display | ![]() |
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Full document | ![]() | 781.2 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rv7S 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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 16408.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700610 / UA159 / Gene: dacA, SMU_1428c / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 202 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AMP / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MLI / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1M sodium malonate pH 5.0, 0.1M sodium acetate trihydrate pH 4.5, 2% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→100 Å / Num. obs: 24283 / % possible obs: 99.8 % / Redundancy: 13.79 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.46 |
Reflection shell | Resolution: 1.94→1.98 Å / Num. unique obs: 8160 / CC1/2: 0.945 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4rv7 Resolution: 1.94→38.97 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 19.5258 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: 33.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→38.97 Å
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Refine LS restraints |
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LS refinement shell |
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