+Open data
-Basic information
Entry | Database: PDB / ID: 2yv8 | ||||||
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Title | Crystal structure of N-terminal domain of human galectin-8 | ||||||
Components | Galectin-8 variant | ||||||
Keywords | SUGAR BINDING PROTEIN / two beta sheets / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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 / MAD / Resolution: 1.92 Å | ||||||
Authors | Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of N-terminal domain of human galectin-8 Authors: Kishishita, S. / Nishino, A. / Kazutaka, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yv8.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yv8.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yv8_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
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Full document | 2yv8_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 2yv8_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2yv8_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yv8 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yv8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18102.559 Da / Num. of mol.: 1 / Fragment: residues 1-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: PK050620-06 / References: UniProt: Q59E97, UniProt: O00214*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Magnesium formate, 15% PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9792, 0.9797, 0.964 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 22, 2006 | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.92→50 Å / Num. obs: 26234 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 5.9 Å2 / Rsym value: 0.054 / Net I/σ(I): 60 | ||||||||||||
Reflection shell | Resolution: 1.92→2.02 Å / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 29.2 / Rsym value: 0.076 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.92→40.57 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 207194.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.3136 Å2 / ksol: 0.355626 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.92→40.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→2.04 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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