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Yorodumi- PDB-6d26: Crystal structure of the prostaglandin D2 receptor CRTH2 with fev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d26 | ||||||
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Title | Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant | ||||||
Components | Prostaglandin D2 receptor 2, Endolysin chimera | ||||||
Keywords | MEMBRANE PROTEIN/ANTAGONIST / GPCR / MEMBRANE PROTEIN-ANTAGONIST complex | ||||||
Function / homology | Function and homology information prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / Prostanoid ligand receptors / negative regulation of male germ cell proliferation / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway ...prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / Prostanoid ligand receptors / negative regulation of male germ cell proliferation / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / G protein-coupled receptor activity / calcium-mediated signaling / chemotaxis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / defense response to bacterium / neuron projection / immune response / G protein-coupled receptor signaling pathway / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.798 Å | ||||||
Authors | Wang, L. / Yao, D. / Deepak, K. / Liu, H. / Gong, W. / Fan, H. / Wei, Z. / Zhang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol. Cell / Year: 2018 Title: Structures of the Human PGD2Receptor CRTH2 Reveal Novel Mechanisms for Ligand Recognition. Authors: Wang, L. / Yao, D. / Deepak, R.N.V.K. / Liu, H. / Xiao, Q. / Fan, H. / Gong, W. / Wei, Z. / Zhang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d26.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d26.ent.gz | 158 KB | Display | PDB format |
PDBx/mmJSON format | 6d26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/6d26 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/6d26 | HTTPS FTP |
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-Related structure data
Related structure data | 6d27C 6c1qS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52228.727 Da / Num. of mol.: 1 Fragment: CRTH2 (UNP residues 1-236), T4 ligase (UNP residues 2-12,61-161), CRTH2 (UNP residues 238-339) Mutation: N25A,G237ADLGLQHR,A1298C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: PTGDR2, CRTH2, DL1R, GPR44, e, T4Tp126 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5Y4, UniProt: D9IEF7 |
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-Non-polymers , 7 types, 21 molecules
#2: Chemical | ChemComp-FSY / | ||||||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-SIN / #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-OLA / | #7: Chemical | ChemComp-PGO / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.03 % |
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Crystal grow | Temperature: 289 K / Method: lipidic cubic phase / pH: 6.5 Details: 100 mM MES, pH 6.5, 100 mM ammonium sulfate, 30% PEG400, 2% P400, 1 mM succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. obs: 19625 / % possible obs: 91.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 68.26 Å2 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.083 / Rrim(I) all: 0.202 / Χ2: 1.153 / Net I/σ(I): 5.3 / Num. measured all: 95491 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6C1Q Resolution: 2.798→29.333 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.66 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 221.59 Å2 / Biso mean: 84.9894 Å2 / Biso min: 38.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.798→29.333 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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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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