+Open data
-Basic information
Entry | Database: PDB / ID: 3vko | |||||||||
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Title | Galectin-8 N-terminal domain in complex with sialyllactosamine | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.08 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 | 3vko.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vko.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vko_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3vko_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3vko_validation.xml.gz | 17 KB | Display | |
Data in CIF | 3vko_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/3vko ftp://data.pdbj.org/pub/pdb/validation_reports/vk/3vko | HTTPS FTP |
-Related structure data
Related structure data | 3vklC 3vkmC 3vknC 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: 17368.109 Da / Num. of mol.: 2 / Fragment: N-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 | #3: Chemical | ChemComp-CL / | #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: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 30%(v/v) PEG400, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 22, 2011 / Details: mirrors |
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 17578 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YV8 Resolution: 2.08→22.6 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.86 / Data cutoff high absF: 1416924 / 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: 58.0525 Å2 / ksol: 0.3264 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.19 Å2 / Biso mean: 44.1042 Å2 / Biso min: 26.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.08→22.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.21 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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