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Open data
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Basic information
Entry | Database: PDB / ID: 5nm2 | ||||||
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Title | A2A Adenosine receptor cryo structure | ||||||
![]() | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weinert, T. / Cheng, R. / James, D. / Gashi, D. / Nogly, P. / Jaeger, K. / Dore, A.S. / Geng, T. / Cooke, R. / Hennig, M. / Standfuss, J. | ||||||
![]() | ![]() Title: Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / ...Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / Dore, A.S. / Geng, T. / Cooke, R.M. / Liang, M. / Prota, A.E. / Panneels, V. / Nogly, P. / Ermler, U. / Schertler, G. / Hennig, M. / Steinmetz, M.O. / Wang, M. / Standfuss, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272 KB | Display | ![]() |
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PDB format | ![]() | 225.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5njmC ![]() 5nlxC ![]() 5nm4C ![]() 5nm5C ![]() 5nqtC ![]() 5nquC ![]() 5o5wC ![]() 5iu4S S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47996.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Gene: ADORA2A, ADORA2, cybC / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 156 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/ZMA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZMA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | ChemComp-ZMA / ![]() | ||||||||
#4: Chemical | ChemComp-OLA / ![]() #5: Chemical | #6: Chemical | #7: Chemical | ![]() #8: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow![]() | Temperature: 291 K / Method: lipidic cubic phase / pH: 5 Details: 0.1M sodium citrate pH 5.0, 0.05M sodium thiocyanate, 28-34% PEG400, 5 mM ZM241385, 2% (v/v) 1,6-hexanedio |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.948→50 Å / Num. obs: 32392 / % possible obs: 87.6 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rrim(I) all: 0.168 / Net I/σ(I): 10.36 |
Reflection shell | Resolution: 1.948→2 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 1670 / CC1/2: 0.461 / Rrim(I) all: 0.918 / % possible all: 61.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5IU4 Resolution: 1.948→41.373 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.04 / 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: 1.948→41.373 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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