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Yorodumi- PDB-3wg3: Crystal structure of Agrocybe cylindracea galectin with blood typ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wg3 | |||||||||
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Title | Crystal structure of Agrocybe cylindracea galectin with blood type A antigen tetraose | |||||||||
Components | Galactoside-binding lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / galectin / galactose binding | |||||||||
Function / homology | Function and homology information DNA nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / polysaccharide binding / positive regulation of apoptotic process / apoptotic process Similarity search - Function | |||||||||
Biological species | Agrocybe cylindracea (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Kuwabara, N. / Hu, D. / Tateno, H. / Makio, H. / Hirabayashi, J. / Kato, R. | |||||||||
Citation | Journal: Febs Lett. / Year: 2013 Title: Conformational change of a unique sequence in a fungal galectin from Agrocybe cylindracea controls glycan ligand-binding specificity. Authors: Kuwabara, N. / Hu, D. / Tateno, H. / Makyio, H. / Hirabayashi, J. / Kato, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wg3.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wg3.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wg3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3wg3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3wg3_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3wg3_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/3wg3 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/3wg3 | HTTPS FTP |
-Related structure data
Related structure data | 3wg1C 3wg2C 3wg4C 1ww7S 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: 19004.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe cylindracea (fungus) / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WY08*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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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: 3 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→35 Å / Num. obs: 98551 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WW7 Resolution: 1.35→30.23 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.946 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.283 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→30.23 Å
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Refine LS restraints |
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