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Yorodumi- PDB-3vy7: Crystal structure of human pancreatic secretory protein ZG16p wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vy7 | ||||||
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Title | Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-serine | ||||||
Components | Zymogen granule membrane protein 16 | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-prism fold | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Kanagawa, M. / Yamaguchi, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vy7.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vy7.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vy7 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vy7 | HTTPS FTP |
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-Related structure data
Related structure data | 3vy6C 3vzeC 3vzfC 3vzgC 3apaS 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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Unit cell |
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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.) Homo sapiens (human) / Gene: ZG16 / Plasmid: pCold-I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60844 | ||
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#2: Chemical | ChemComp-SER / | ||
#3: Sugar | ChemComp-MAN / | ||
#4: Chemical | #5: 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: 2.1 Å3/Da / Density % sol: 41.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2011 |
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: 2.1→50 Å / Num. obs: 8123 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3apa Resolution: 2.14→45.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.188 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.209 / 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: 20.355 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→45.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.139→2.194 Å / Total num. of bins used: 20
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