+Open data
-Basic information
Entry | Database: PDB / ID: 5yre | |||||||||||||||
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Title | Crystal structure of PPL3A | |||||||||||||||
Components | (PPL3-A) x 2 | |||||||||||||||
Keywords | 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 Function and homology information | |||||||||||||||
Biological species | Pteria penguin (invertebrata) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||||||||
Authors | Nakae, S. / Shionyu, M. / Ogawa, T. / Shirai, T. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Proteins / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yre.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yre.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yre_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 5yre_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 5yre_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5yre_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yre ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yre | HTTPS FTP |
-Related structure data
Related structure data | 5yrfC 5yrgC 5yrhC 5yriC 5yrjC 5yrkSC 5yrlC 5yrmC S: Starting model for refinement C: citing same article (ref.) |
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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: 15754.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pteria penguin (invertebrata) / References: UniProt: B6F0T7 | ||||||
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#2: Protein | Mass: 15722.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pteria penguin (invertebrata) / References: UniProt: B6F0T7 | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | The N-terminus of subunit after signal peptide removal is Gln20-Val21 from mRNA, but is changed to ...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. The genebank accession for PPL3-a is AB425240.2. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.4 % |
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Crystal grow | Temperature: 293 K / Method: small tubes Details: 0.2M ammonium sulfate, 25%(w/v) PEG 3350, 0.1M Tris/bis-Tris buffer pH 5.5 microgravity environments on ISS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 44177 / % possible obs: 90.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.016 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 5714 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YRK Resolution: 1.4→19.739 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→19.739 Å
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Refine LS restraints |
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LS refinement shell |
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