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- PDB-3vy6: Crystal structure of human pancreatic secretory protein ZG16p wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vy6 | |||||||||
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Title | Crystal structure of human pancreatic secretory protein ZG16p with laminaribiose | |||||||||
![]() | Zymogen granule membrane protein 16 | |||||||||
![]() | SUGAR BINDING PROTEIN / beta-prism fold | |||||||||
Function / homology | ![]() suppression of symbiont entry into host / mucus layer / zymogen granule membrane / peptidoglycan binding / Golgi lumen / protein transport / carbohydrate binding / collagen-containing extracellular matrix / defense response to Gram-positive bacterium / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kanagawa, M. / Yamaguchi, Y. | |||||||||
![]() | ![]() Title: Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin Authors: Kanagawa, M. / Liu, Y. / Hanashima, S. / Ikeda, A. / Chai, W. / Nakano, Y. / Kojima-Aikawa, K. / Feizi, T. / Yamaguchi, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.1 KB | Display | ![]() |
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PDB format | ![]() | 29.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 751 KB | Display | ![]() |
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Full document | ![]() | 751.8 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vy7C ![]() 3vzeC ![]() 3vzfC ![]() 3vzgC ![]() 3apaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15501.401 Da / Num. of mol.: 1 / Fragment: UNP residues 21-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.09M MES (pH 6.5), 0.09M sodium phosphate, 0.09M potassium phosphate, 1.8M sodium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 9347 / % possible obs: 99.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.1 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3apa Resolution: 2→45.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.761 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.174 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.838 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.996→2.048 Å / Total num. of bins used: 20
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