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- PDB-6yxg: Cryogenic human adiponectin receptor 2 (ADIPOR2) with Tb-XO4 liga... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yxg | ||||||||||||
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Title | Cryogenic human adiponectin receptor 2 (ADIPOR2) with Tb-XO4 ligand determined by Serial Crystallography (SSX) using CrystalDirect | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Healey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: An automated platform for structural analysis of membrane proteins through serial crystallography. Authors: Healey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Cong, X. / Golebiowski, J. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.2 KB | Display | ![]() |
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PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yx9C ![]() 6yxdC ![]() 6yxfC ![]() 6yxhC ![]() 5lwyS 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 / Antibody , 2 types, 2 molecules AH
#1: Protein | ![]() Mass: 33097.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 25421.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 33 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/7MT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/7MT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | ChemComp-OLA / ![]() | ||||
#5: Chemical | ChemComp-OLB / ( #6: Chemical | #7: 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: 3.55 Å3/Da / Density % sol: 65.32 % |
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Crystal grow![]() | Temperature: 293 K / Method: lipidic cubic phase Details: 30 or 50 nL bolus overlaid with 600 nL precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, ...Details: 30 or 50 nL bolus overlaid with 600 nL precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0. 30-150 nL of Tb-XO4 soaking solution with a final conc. of 5 - 25 mM was delivered onto LCP crystallisation drop. Crystallisation experiments were carried out at the HTX facility of EMBL Grenoble. LCP bolus were harvested automatically at cryogenic condition using CrystalDirect technology. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3→50 Å / Num. obs: 32012 / % possible obs: 100 % / Redundancy: 34.82 % / CC1/2: 0.99 / Net I/σ(I): 7.33 |
Reflection shell | Resolution: 3→3.1 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 2150 / CC1/2: 0.3 / % possible all: 100 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5LWY Resolution: 3.01→48 Å / Cor.coef. Fo:Fc: 0.81 / Cor.coef. Fo:Fc free: 0.831 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377
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Displacement parameters | Biso max: 300 Å2 / Biso mean: 81.27 Å2 / Biso min: 48.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.01→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.1 Å / Rfactor Rfree error: 0
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