+Open data
-Basic information
Entry | Database: PDB / ID: 3apa | ||||||
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Title | Crystal structure of human pancreatic secretory protein ZG16p | ||||||
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: 1.65 Å | ||||||
Authors | Kanagawa, M. / Satoh, T. / Nakano, Y. / Kojima-Aikawa, K. / Yamaguchi, Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 Title: Crystal structures of human secretory proteins ZG16p and ZG16b reveal a Jacalin-related beta-prism fold Authors: Kanagawa, M. / Satoh, T. / Ikeda, A. / Nakano, Y. / Yagi, H. / Kato, K. / Kojima-Aikawa, K. / Yamaguchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3apa.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3apa.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 3apa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/3apa ftp://data.pdbj.org/pub/pdb/validation_reports/ap/3apa | HTTPS FTP |
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-Related structure data
Related structure data | 3aqgC 1c3kS 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(MBP fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60844 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.09 Å3/Da / Density % sol: 41.23 % |
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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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2009 |
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: 1.65→50 Å / Num. obs: 16473 / % possible obs: 99.3 % / Redundancy: 14 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 6.2 / Num. unique all: 819 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3K Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.998 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 18.748 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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