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Yorodumi- PDB-3zvx: STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zvx | |||||||||
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Title | STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH A TRIMANNOSIDE | |||||||||
Components | LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / PLANT LECTIN / N-GLYCAN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | PLATYPODIUM ELEGANS (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Benevides, R.G. / Ganne, G. / Unverzagt, C. / Cavada, B.S. / Breton, C. / Varrot, A. / Imberty, A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: A Lectin from Platypodium Elegans with Unusual Specificity and Affinity for Asymmetric Complex N-Glycans. Authors: Benevides, R.G. / Ganne, G. / Simoes, R.D.C. / Schubert, V. / Niemietz, M. / Unverzagt, C. / Chazalet, V. / Breton, C. / Varrot, A. / Cavada, B.S. / Imberty, A. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zvx.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zvx.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/3zvx ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zvx | HTTPS FTP |
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-Related structure data
Related structure data | 3zyrC 1n3oS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9105, -0.24247, 0.33497), Vector: |
-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 29314.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLATYPODIUM ELEGANS (plant) / Description: BRASILIAN FLORA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: G1EUI6*PLUS #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 334 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | GENBANK ACCESSION JN133278 |
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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: 2.18 Å3/Da / Density % sol: 43.55 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 1.5 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5, 12% GLYCEROL. GLYCEROL CONCENTRATION WAS INCREASED TO 25% FOR CRYOPROTECTION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.6 Å / Num. obs: 28894 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N3O Resolution: 2.1→42.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.055 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-7 AND 250-261 ARE DISORDERED AND WERE NOT MODELLED. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
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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: 24.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.25 Å
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Refine LS restraints |
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