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Open data
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Basic information
Entry | Database: PDB / ID: 7mg2 | |||||||||
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Title | Concanavalin A crystallized in the presence of Man-8 | |||||||||
![]() | Concanavalin-A | |||||||||
![]() | SUGAR BINDING PROTEIN/DNA / Lectin / SUGAR BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Partridge, B.E. / Winegar, P.H. / Mirkin, C.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Redefining Protein Interfaces within Protein Single Crystals with DNA. Authors: Partridge, B.E. / Winegar, P.H. / Han, Z. / Mirkin, C.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.5 KB | Display | ![]() |
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Full document | ![]() | 410.5 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mg1C ![]() 7mg3C ![]() 7mg4C ![]() 7mg5C ![]() 7mg6C ![]() 7mg7C ![]() 7mg8C ![]() 7mg9C ![]() 7mgaC ![]() 7mgbC ![]() 7mgcC ![]() 7mgdC ![]() 1jbcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and mannose-squaramide (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and mannose-squaramide (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium chloride hexahydrate, 0.05 M MES (pH 6.5), 17% w/v PEG 4000). Reservoir contained 70 uL of crystallization condition. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→62.06 Å / Num. obs: 21234 / % possible obs: 99.8 % / Redundancy: 9.11 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 2.5465 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 8.95 % / Rmerge(I) obs: 0.63 / Num. unique obs: 3218 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JBC Resolution: 1.8→62.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.304 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The authors state that the electron density was not observed for the molecule Man-8, though it was present in the crystallization solution from which this crystal of ConA was obtained. ...Details: The authors state that the electron density was not observed for the molecule Man-8, though it was present in the crystallization solution from which this crystal of ConA was obtained. HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→62.06 Å
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Refine LS restraints |
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