+Open data
-Basic information
Entry | Database: PDB / ID: 7bsm | ||||||
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Title | Mevo lectin complex with 2alpha-mannobiose | ||||||
Components | lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure | ||||||
Function / homology | Jacalin-like lectin domain superfamily / 2alpha-alpha-mannobiose / ALANINE / alpha-D-mannopyranose / Jacalin-type lectin domain-containing protein Function and homology information | ||||||
Biological species | Methanococcus voltae (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
Funding support | India, 1items
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Citation | Journal: Glycobiology / Year: 2021 Title: Structural and related studies on Mevo lectin from Methanococcus voltae A3: the first thorough characterization of an archeal lectin and its interactions. Authors: Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bsm.cif.gz | 371.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bsm.ent.gz | 302.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/7bsm ftp://data.pdbj.org/pub/pdb/validation_reports/bs/7bsm | HTTPS FTP |
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-Related structure data
Related structure data | 7bsbSC 7bsnC 7bt8C 7bt9C 7bthC 7btlC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15783.812 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus voltae (strain ATCC BAA-1334 / A3) (archaea) Strain: ATCC BAA-1334 / A3 / Gene: Mvol_0737 / Production host: Escherichia coli (E. coli) / References: UniProt: D7DTD6 #2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose #3: Sugar | #4: Chemical | ChemComp-ALA / | Has ligand of interest | Y | |
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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: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 296 K / Method: microbatch Details: 6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000 PH range: 5.8-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9767 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→96.25 Å / Num. obs: 70202 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.22 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.8→2.95 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10083 / CC1/2: 0.73 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BSB Resolution: 2.8→96.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.929 / ESU R Free: 0.35 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→96.25 Å
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Refine LS restraints |
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