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Yorodumi- PDB-8end: Crystal structure of LGR ligand alpha2/beta5 from C. elegans in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8end | ||||||
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Title | Crystal structure of LGR ligand alpha2/beta5 from C. elegans in crystal form 1 (SeMet) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / cystine-knot hormone (CKH) / leucine-rich repeat-containing G protein-coupled receptor (LGR) / evolution / glycoprotein hormone (GPH) / thyrostimulin | ||||||
Function / homology | Function and homology information Hormone ligand-binding receptors / G alpha (s) signalling events / hormone activity / G protein-coupled receptor signaling pathway / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å | ||||||
Authors | Gong, Z. / Hendrickson, W.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Crystal structure of LGR ligand alpha2/beta5 from Caenorhabditis elegans with implications for the evolution of glycoprotein hormones Authors: Gong, Z. / Wang, W. / El Omari, K. / Lebedev, A.A. / Clarke, O.B. / Hendrickson, W.A. #1: Journal: To be Published Title: Combining AlphaFold and phenix.mr_rosetta for solving challenging crystal structures Authors: Wang, W. / Gong, Z. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8end.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8end.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 8end.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/8end ftp://data.pdbj.org/pub/pdb/validation_reports/en/8end | HTTPS FTP |
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-Related structure data
Related structure data | 8enbSC 8enfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10706.149 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Homo sapiens (human) / References: UniProt: A0T3A2 |
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#2: Protein | Mass: 11683.888 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gpb5, CELE_T23B12.8, T23B12.8 / Production host: Homo sapiens (human) / References: UniProt: A7DT38 |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.28 Å3/Da / Density % sol: 76.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M MES, pH 6.0, 40% w/v PEG200, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.54→49.03 Å / Num. obs: 4990 / % possible obs: 92.8 % / Redundancy: 494 % / Biso Wilson estimate: 171.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.455 / Net I/σ(I): 21 |
Reflection shell | Resolution: 3.54→3.89 Å / Num. unique obs: 413 / CC1/2: 0.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8ENB Resolution: 3.54→46.27 Å / SU ML: 0.4615 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.3133 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 184.97 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.54→46.27 Å
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Refine LS restraints |
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LS refinement shell |
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