+Open data
-Basic information
Entry | Database: PDB / ID: 3ca0 | |||||||||
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Title | Sambucus nigra agglutinin II (SNA-II), hexagonal crystal form | |||||||||
Components | Agglutinin II | |||||||||
Keywords | SUGAR BINDING PROTEIN / Plant protein / BETA-TREFOIL / RICIN-B DOMAIN / GLYCOSYLATION / Glycoprotein / Lectin | |||||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation Similarity search - Function | |||||||||
Biological species | Sambucus nigra (European elder) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Maveyraud, L. / Niwa, H. / Guillet, V. / Palmer, R.A. / Reynolds, C.D. / Mourey, L. | |||||||||
Citation | Journal: Proteins / Year: 2009 Title: Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra Authors: Maveyraud, L. / Niwa, H. / Guillet, V. / Svergun, D.I. / Konarev, P.V. / Palmer, R.A. / Peumans, W.J. / Rouge, P. / Van Damme, E.J. / Reynolds, C.D. / Mourey, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ca0.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ca0.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ca0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3ca0 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3ca0 | HTTPS FTP |
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-Related structure data
Related structure data | 3c9zC 3ca1C 3ca3C 3ca4C 3ca5C 3ca6C 3cahC 2aaiS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28439.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sambucus nigra (European elder) / Tissue: BARK / References: UniProt: P33183 |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 343 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE ELECTRON DENSITY OF THE STRUCTURE INDICATES CLEARLY THAT THE AMINO ACID AT ...AUTHORS STATE THAT THE ELECTRON DENSITY OF THE STRUCTURE INDICATES CLEARLY THAT THE AMINO ACID AT POSITION 224 IS A LEU AND NOT A HIS. |
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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: 6.52 Å3/Da / Density % sol: 81.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 M, SODIUM ACETATE 100 mM, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.937 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2002 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→51.3 Å / Num. all: 57308 / Num. obs: 57308 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5977 / Rsym value: 0.324 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: chain B of ricin, PDN entry 2AAI Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.696 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.086 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.658 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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