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Open data
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Basic information
Entry | Database: PDB / ID: 7btl | ||||||
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Title | Mevo lectin complex with mannopentose | ||||||
![]() | lectin | ||||||
![]() | SUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure | ||||||
Function / homology | Jacalin-like lectin domain superfamily / 6alpha-alpha-mannobiose / alpha-D-mannopyranose / Jacalin-type lectin domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.6 KB | Display | ![]() |
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PDB format | ![]() | 163.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bsbC ![]() 7bsmC ![]() 7bsnC ![]() 7bt8SC ![]() 7bt9C ![]() 7bthC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 7 molecules BGADEFC
#1: Protein | Mass: 15210.124 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-1334 / A3 / Gene: Mvol_0737 / Production host: ![]() ![]() |
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-Sugars , 4 types, 8 molecules ![](data/chem/img/MAN.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | #5: Sugar | |
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-Non-polymers , 2 types, 164 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 59.48 % |
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Crystal grow | Temperature: 296 K / Method: microbatch / pH: 6 Details: 6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→85.04 Å / Num. obs: 71908 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10315 / CC1/2: 0.75 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7BT8 Resolution: 2.25→85.034 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.228 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: 32.851 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→85.034 Å
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Refine LS restraints |
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