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Open data
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Basic information
Entry | Database: PDB / ID: 8wmg | ||||||
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Title | Structure of ConA/Man3 | ||||||
![]() | Concanavalin-A | ||||||
![]() | SUGAR BINDING PROTEIN / Mannose binding protein / Concanavalin-A | ||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, L. / Chen, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Rational design of inducing ligands with three-dimensional supramolecular interactions to build protein crystalline frameworks. Authors: Li, L. / Chen, G. | ||||||
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 | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8wmkC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 5 molecules AB![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Author stated: This sequence is a mature form of the provided reference P02866. Source: (natural) ![]() ![]() #4: Sugar | |
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-Non-polymers , 5 types, 138 molecules ![](data/chem/img/WRW.gif)
![](data/chem/img/ETA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ETA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-WRW / | ||||||
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#3: Chemical | #5: Chemical | #6: Chemical | #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: 4.23 Å3/Da / Density % sol: 70.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: buffer: 20 mM HEPES, 5 mM CaCl2, 5 mM MnCl2, pH = 7.5, Precipitant: 200 mM Ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→81.04 Å / Num. obs: 60702 / % possible obs: 98.5 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.047 / Rrim(I) all: 0.15 / Χ2: 0.96 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8918 / CC1/2: 0.855 / Rpim(I) all: 0.315 / Rrim(I) all: 0.993 / Χ2: 0.84 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.677 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→66.02 Å
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