+Open data
-Basic information
Entry | Database: PDB / ID: 8czk | ||||||
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Title | Human LanCL1 bound to GSH and Dhb-Erk peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / LanCL1 / lanthipeptide biosynthesis / Erk | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 | 8czk.cif.gz | 180.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8czk.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 8czk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/8czk ftp://data.pdbj.org/pub/pdb/validation_reports/cz/8czk | HTTPS FTP |
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-Related structure data
Related structure data | 8czlC 8d0vC 8d19C 3e6uS 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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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 Source: (gene. exp.) Homo sapiens (human) / Gene: LANCL1, GPR69A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43813, glutathione transferase #2: Protein/peptide | Mass: 710.775 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The authors report that chain D displays a better fit to electron density for Try 6 than chain C Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #5: 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: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.70-0.75 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: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→92.5 Å / Num. obs: 75709 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Rrim(I) all: 0.126 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.914→1.92 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.284 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 809 / CC1/2: 0.785 / Rpim(I) all: 0.438 / Rrim(I) all: 1.36 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E6U Resolution: 1.91→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.568 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.131 / 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: 31.31 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→25 Å
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Refine LS restraints |
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