+Open data
-Basic information
Entry | Database: PDB / ID: 7bsb | ||||||
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Title | Mevo lectin- Native form-2 | ||||||
Components | lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure | ||||||
Function / homology | Jacalin-like lectin domain superfamily / Jacalin-type lectin domain-containing protein Function and homology information | ||||||
Biological species | Methanococcus voltae (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 7bsb.cif.gz | 373.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bsb.ent.gz | 304.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bsb_validation.pdf.gz | 554.5 KB | Display | wwPDB validaton report |
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Full document | 7bsb_full_validation.pdf.gz | 571.2 KB | Display | |
Data in XML | 7bsb_validation.xml.gz | 69.8 KB | Display | |
Data in CIF | 7bsb_validation.cif.gz | 92.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/7bsb ftp://data.pdbj.org/pub/pdb/validation_reports/bs/7bsb | HTTPS FTP |
-Related structure data
Related structure data | 7bsmC 7bsnC 7bt8C 7bt9C 7bthC 7btlC 4znoS 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: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.82 Å3/Da / Density % sol: 56.35 % |
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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: 5.8-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→96.12 Å / Num. obs: 102790 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14786 / CC1/2: 0.828 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZNO Resolution: 2.45→70.599 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.231 / Average fsc free: 0.8751 / Average fsc work: 0.8953 / Cross valid method: FREE R-VALUE / ESU R: 0.37 / ESU R Free: 0.266 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.684 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→70.599 Å
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Refine LS restraints |
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