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Open data
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Basic information
Entry | Database: PDB / ID: 5yrg | |||||||||||||||
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Title | PPL3A-isomaltose complex | |||||||||||||||
![]() | (PPL3-A) x 2 | |||||||||||||||
![]() | SUGAR BINDING PROTEIN / Lectin / Biomineralization / Post-translational modification / Calcite / Docking simulation | |||||||||||||||
Function / homology | Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / carbohydrate binding / Jacalin-related lectin![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Nakae, S. / Shionyu, M. / Ogawa, T. / Shirai, T. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization Authors: Nakae, S. / Shionyu, M. / Ogawa, T. / Shirai, T. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.7 KB | Display | ![]() |
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PDB format | ![]() | 60.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yreC ![]() 5yrfC ![]() 5yrhC ![]() 5yriC ![]() 5yrjC ![]() 5yrkSC ![]() 5yrlC ![]() 5yrmC S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 15754.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#2: Protein | Mass: 15722.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | The genebank accession for PPL3-a is AB425240.2. The N-terminus of subunit after signal peptide ...The genebank accession for PPL3-a is AB425240.2. The N-terminus of subunit after signal peptide removal is Gln20-Val21 from mRNA, but is changed to pGlu20-Val21 or Gln20-Ile21 because of post-translational modifications. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium sulfate, 25%(w/v) PEG 3350, 0.1M Tris buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 44443 / % possible obs: 99.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 6432 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YRK Resolution: 1.5→19.842 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.842 Å
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Refine LS restraints |
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LS refinement shell |
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