+Open data
-Basic information
Entry | Database: PDB / ID: 3e6u | ||||||
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Title | Crystal structure of Human LanCL1 | ||||||
Components | LanC-like protein 1 | ||||||
Keywords | SIGNALING PROTEIN / Alpha Barrel / Cytoplasm | ||||||
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 / SAD / Resolution: 2.6 Å | ||||||
Authors | Zhang, W. / Zhu, G. / Li, X. / Rao, Z. / Zhang, C. | ||||||
Citation | Journal: Genes Dev. / Year: 2009 Title: Structure of human lanthionine synthetase C-like protein 1 and its interaction with Eps8 and glutathione Authors: Zhang, W. / Wang, L. / Liu, Y. / Xu, J. / Zhu, G. / Cang, H. / Li, X. / Bartlam, M. / Hensley, K. / Li, G. / Rao, Z. / Zhang, X.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e6u.cif.gz | 320.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6u.ent.gz | 262.4 KB | Display | PDB format |
PDBx/mmJSON format | 3e6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6u_validation.pdf.gz | 468.9 KB | Display | wwPDB validaton report |
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Full document | 3e6u_full_validation.pdf.gz | 518.2 KB | Display | |
Data in XML | 3e6u_validation.xml.gz | 61.9 KB | Display | |
Data in CIF | 3e6u_validation.cif.gz | 84.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6u ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 46884.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LANCL1 / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O43813 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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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: 6.189906 Å3/Da / Density % sol: 80.128937 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.5M ammonium formate, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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Detector | Date: Nov 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→32.6 Å / Num. obs: 130560 / % possible obs: 92.22 % |
Reflection shell | Resolution: 2.6→2.667 Å / % possible all: 84.22 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→32.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.467 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.772 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→32.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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