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Yorodumi- PDB-6mh8: High-viscosity injector-based Pink Beam Serial Crystallography of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mh8 | |||||||||||||||||||||||||||||||||
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Title | High-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source | |||||||||||||||||||||||||||||||||
Components | Adenosine receptor A2a, Soluble cytochrome b562 chimeric constructAdenosine A2A receptor | |||||||||||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / Pink beam serial crystallography | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information 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 / sensory perception / positive regulation of urine volume ...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 / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, dopaminergic / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / response to inorganic substance / cellular defense response / prepulse inhibition / phagocytosis / positive regulation of apoptotic signaling pathway / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / electron transfer activity / periplasmic space / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / dendrite / neuronal cell body / lipid binding / glutamatergic synapse / apoptotic process / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | |||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | |||||||||||||||||||||||||||||||||
Authors | Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. ...Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhan, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W. | |||||||||||||||||||||||||||||||||
Funding support | United States, 10items
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Citation | Journal: Iucrj / Year: 2019 Title: High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / ...Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mh8.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mh8.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/6mh8 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/6mh8 | HTTPS FTP |
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-Related structure data
Related structure data | 6mh6C 5uviS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49974.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADORA2A, ADORA2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7 |
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#2: Chemical | ChemComp-ZMA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 5 / Details: sodium citrate pH 5.0, PEG 400, sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.033-1.67 | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Jun 24, 2017 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 4.2→50 Å / Num. obs: 4021 / % possible obs: 87.8 % / Redundancy: 11.5 % / R split: 0.27 / Net I/σ(I): 4.5 | |||||||||
Reflection shell | Resolution: 4.2→4.3 Å / R split: 0.262 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UVI Resolution: 4.2→50 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.798 / SU B: 84.914 / SU ML: 1.114 / Cross valid method: THROUGHOUT / ESU R Free: 1.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.074 Å2
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Refinement step | Cycle: 1 / Resolution: 4.2→50 Å
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Refine LS restraints |
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