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Open data
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Basic information
Entry | Database: PDB / ID: 8szo | |||||||||
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Title | Canavalia villosa lectin in complex with alpha-methyl-mannoside | |||||||||
![]() | Canavalia villosa lectin | |||||||||
![]() | SUGAR BINDING PROTEIN / Carbohydrate binding protein / Plant lectin / beta-sandwich / pro-inflammatory / PLANT PROTEIN | |||||||||
Function / homology | methyl alpha-D-mannopyranoside / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cavada, B.S. / Lossio, C.F. / Pinto-Junior, V.R. / Osterne, V.J.S. / Oliveira, M.V. / Neco, A.H.B. / Nascimento, K.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Lectin from Canavalia villosa seeds: A glucose/mannose-specific protein and a new tool for inflammation studies. Authors: Lossio, C.F. / Moreira, C.G. / Amorim, R.M.F. / Nobre, C.S. / Silva, M.T.L. / Neto, C.C. / Pinto-Junior, V.R. / Silva, I.B. / Campos, J. / Assreuy, A.M.S. / Cavada, B.S. / Nascimento, K.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.4 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/MMA.gif)
![](data/chem/img/MMA.gif)
#1: Protein | Mass: 25685.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The residues S117, N118, S119 and T120 in the coordinate sequence are located in a loop region of the tertiary structure and were not detected due to lack of electron density on this ...Details: The residues S117, N118, S119 and T120 in the coordinate sequence are located in a loop region of the tertiary structure and were not detected due to lack of electron density on this specific region. This data deficiency is frequently observed in other ConA-like lectins structures solved by macromolecular crystallography. The sample sequence displays the full 237 amino acid of the protein. Source: (natural) ![]() |
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#4: Sugar | ChemComp-MMA / |
-Non-polymers , 4 types, 91 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-GOL / |
#6: 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: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.2 Details: PEG1000, potassium citrate phosphate, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→27.48 Å / Num. obs: 8301 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.056 / Rrim(I) all: 0.126 / Net I/σ(I): 8.9 / Num. measured all: 40674 |
Reflection shell | Resolution: 2.5→2.64 Å / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.433 / Num. measured all: 5399 / Num. unique obs: 1200 / CC1/2: 0.867 / Rpim(I) all: 0.224 / Rrim(I) all: 0.489 / Net I/σ(I) obs: 3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→27.48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.6292 Å / Origin y: 14.4776 Å / Origin z: 11.3444 Å
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Refinement TLS group | Selection details: all |