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Yorodumi- PDB-3vkl: Protease-resistant mutant form of human Galectin-8 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vkl | |||||||||
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Title | Protease-resistant mutant form of human Galectin-8 in complex with two lactose molecules | |||||||||
Components | Galectin-8 | |||||||||
Keywords | SUGAR BINDING PROTEIN / BETA-SANDWICH / CARBOHYDRATE BINDING / OLIGOSACCHARIDE | |||||||||
Function / homology | Function and homology information lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Kamitori, S. / Yoshida, H. | |||||||||
Citation | Journal: Febs J. / Year: 2012 Title: X-ray structure of a protease-resistant mutant form of human galectin-8 with two carbohydrate recognition domains Authors: Yoshida, H. / Yamashita, S. / Teraoka, M. / Itoh, A. / Nakakita, S. / Nishi, N. / Kamitori, S. | |||||||||
History |
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Remark 650 | HELIX Determination method: Author determined | |||||||||
Remark 700 | SHEET Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vkl.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vkl.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vkl_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3vkl_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3vkl_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 3vkl_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/3vkl ftp://data.pdbj.org/pub/pdb/validation_reports/vk/3vkl | HTTPS FTP |
-Related structure data
Related structure data | 3vkmC 3vknC 3vkoC 4fqzC 2yv8S 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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2 |
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Unit cell |
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Details | AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS MONOMER OR PSEUDO-DIMER OR UNKNOWN. |
-Components
#1: Protein | Mass: 33110.141 Da / Num. of mol.: 2 Fragment: N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214 #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose #3: Chemical | ChemComp-EDO / #4: 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: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2-3%(v/v) 1,4-dioxane, 9-10%(w/v) PEG20000, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 13, 2009 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 22008 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1093 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YV8 Resolution: 2.55→39.75 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.8 / Data cutoff high absF: 121679168 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.8865 Å2 / ksol: 0.3016 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.8 Å2 / Biso mean: 40.8378 Å2 / Biso min: 15.33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→39.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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