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Open data
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Basic information
Entry | Database: PDB / ID: 6djz | |||||||||
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Title | Human sigma-1 receptor bound to haloperidol | |||||||||
![]() | Sigma non-opioid intracellular receptor 1 | |||||||||
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Function / homology | ![]() G protein-coupled opioid receptor activity / nuclear outer membrane / anchoring junction / lipid transport / nuclear inner membrane / protein homotrimerization / regulation of neuron apoptotic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schmidt, H.R. / Kruse, A.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for sigma1receptor ligand recognition. Authors: Schmidt, H.R. / Betz, R.M. / Dror, R.O. / Kruse, A.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.2 KB | Display | ![]() |
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PDB format | ![]() | 114.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dk0C ![]() 6dk1C ![]() 5hk1S 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 on special symmetry positions |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 25447.879 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 60 molecules ![](data/chem/img/GMJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-GOL / ![]() #5: Chemical | ChemComp-OLC / ( #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow![]() | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.4 Details: Protein was reconstituted in cubic phase by mixing with a 1:1.5 (w:w) protein:lipid ratio. Lipid used was a 10:1 (w:w) mix of monoolein with cholesterol. Crystals were grown in 500 mM ...Details: Protein was reconstituted in cubic phase by mixing with a 1:1.5 (w:w) protein:lipid ratio. Lipid used was a 10:1 (w:w) mix of monoolein with cholesterol. Crystals were grown in 500 mM lithium sulfate, 42% PEG 300, 1% hexanediol, 100 mM MES pH 6.4 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.08→50 Å / Num. obs: 22196 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.994 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.08→3.3 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.4 / CC1/2: 0.164 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5HK1 Resolution: 3.084→40.509 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.084→40.509 Å
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Refine LS restraints |
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LS refinement shell |
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