+Open data
-Basic information
Entry | Database: PDB / ID: 8d19 | ||||||
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Title | Human LanCL1 bound to GSH | ||||||
Components | Glutathione S-transferase LANCL1 | ||||||
Keywords | SIGNALING PROTEIN / LanCL1 / lanthibiotic cyclase | ||||||
Function / homology | Function and homology information peptide modification / glutathione binding / cellular detoxification / low-density lipoprotein particle receptor binding / glutathione transferase / glutathione transferase activity / G protein-coupled receptor activity / SH3 domain binding / carbohydrate metabolic process / G protein-coupled receptor signaling pathway ...peptide modification / glutathione binding / cellular detoxification / low-density lipoprotein particle receptor binding / glutathione transferase / glutathione transferase activity / G protein-coupled receptor activity / SH3 domain binding / carbohydrate metabolic process / G protein-coupled receptor signaling pathway / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Ongpipattanakul, C. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: The mechanism of thia-Michael addition catalyzed by LanC enzymes. Authors: Ongpipattanakul, C. / Liu, S. / Luo, Y. / Nair, S.K. / van der Donk, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d19.cif.gz | 194 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d19.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 8d19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d19_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8d19_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8d19_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 8d19_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/8d19 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/8d19 | HTTPS FTP |
-Related structure data
Related structure data | 8czkC 8czlC 8d0vC 3e6uS C: citing same article (ref.) S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47504.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LanCL1 used for crystallization including expression tags. Source: (gene. exp.) Homo sapiens (human) / Gene: LANCL1, GPR69A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43813, glutathione transferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 282.15 K / Method: vapor diffusion, hanging drop Details: 0.7-0.75 M succinic acid pH 7.0, 0.1 M bis-tris propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.512→92.401 Å / Num. obs: 150903 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.512→1.517 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1476 / CC1/2: 0.813 / Rpim(I) all: 0.341 / Rrim(I) all: 1.142 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E6U Resolution: 1.52→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.245 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.88 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→25 Å
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Refine LS restraints |
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