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Open data
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Basic information
Entry | Database: PDB / ID: 7mgb | |||||||||
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Title | Concanavalin A bound to a DNA glycoconjugate, A(Man-T)AT | |||||||||
![]() | Concanavalin-A | |||||||||
![]() | SUGAR BINDING PROTEIN/DNA / Lectin / DNA complex / SUGAR BINDING PROTEIN / 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 | ![]() | 186 KB | Display | ![]() |
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PDB format | ![]() | 145 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.4 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mg1C ![]() 7mg2C ![]() 7mg3C ![]() 7mg4C ![]() 7mg5C ![]() 7mg6C ![]() 7mg7C ![]() 7mg8C ![]() 7mg9C ![]() 7mgaC ![]() 7mgcC ![]() 7mgdC ![]() 5cnaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Sugar | ChemComp-MMA / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Sitting drop comprising 1 uL of Concanavalin A (40 uM) and A(Man-T)AT (160 uM) + 1 uL crystallization condition (Helix screen, condition H10: 0.05 M lithium sulfate, 0.03 M magnesium sulfate ...Details: Sitting drop comprising 1 uL of Concanavalin A (40 uM) and A(Man-T)AT (160 uM) + 1 uL crystallization condition (Helix screen, condition H10: 0.05 M lithium sulfate, 0.03 M magnesium sulfate heptahydrate, 0.05 M bis Tris (pH 8), 15% w/v PEG 3350). 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: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→84.79 Å / Num. obs: 33189 / % possible obs: 94.87 % / Redundancy: 7.43 % / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.158 / Net I/σ(I): 3.9634 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 7.53 % / Rmerge(I) obs: 0.83 / Num. unique obs: 5282 / Rrim(I) all: 0.888 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CNA Resolution: 2.45→84.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.088 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE AUTHORS STATE THAT THE COORDINATES OF THE DNA COULD NOT BE RESOLVED IN THE ELECTRON DENSITY, PUTATIVELY DUE TO DISORDER, BUT ITS BINDING IS CONFIRMED BY THE OBSERVATION OF THE ...Details: THE AUTHORS STATE THAT THE COORDINATES OF THE DNA COULD NOT BE RESOLVED IN THE ELECTRON DENSITY, PUTATIVELY DUE TO DISORDER, BUT ITS BINDING IS CONFIRMED BY THE OBSERVATION OF THE METHYLMANNOSE (THIS IS ACTUALLY PART OF A MANNOSE-SQUARAMIDE LINKER COVALENTLY BOUND TO THE DNA). 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: 34.416 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→84.79 Å
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Refine LS restraints |
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