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Yorodumi- PDB-3woc: Crystal structure of a prostate-specific WGA16 glycoprotein lecti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3woc | ||||||
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Title | Crystal structure of a prostate-specific WGA16 glycoprotein lectin, form II | ||||||
Components | hypothetical protein | ||||||
Keywords | UNKNOWN FUNCTION / beta-prism-fold | ||||||
Function / homology | Function and homology information Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Garenaux, E. / Kanagawa, M. / Tsuchiyama, T. / Hori, K. / Kanazawa, T. / Goshima, A. / Chiba, M. / Yasue, H. / Ikeda, A. / Yamaguchi, Y. ...Garenaux, E. / Kanagawa, M. / Tsuchiyama, T. / Hori, K. / Kanazawa, T. / Goshima, A. / Chiba, M. / Yasue, H. / Ikeda, A. / Yamaguchi, Y. / Sato, C. / Kitajima, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Discovery, Primary, and Crystal Structures and Capacitation-related Properties of a Prostate-derived Heparin-binding Protein WGA16 from Boar Sperm Authors: Garenaux, E. / Kanagawa, M. / Tsuchiyama, T. / Hori, K. / Kanazawa, T. / Goshima, A. / Chiba, M. / Yasue, H. / Ikeda, A. / Yamaguchi, Y. / Sato, C. / Kitajima, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3woc.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3woc.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 3woc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/3woc ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3woc | HTTPS FTP |
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-Related structure data
Related structure data | 3wobC 3aqgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 16354.448 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8IK66*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-DIO / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES pH 6.5, 1.6M (NH4)2SO4, 10%(v/v) 1,4-dioxane, 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: Jan 30, 2013 |
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: 2.4→87.04 Å / Num. obs: 35861 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AQG Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.865 / SU B: 12.965 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.347 / 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: 39.536 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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