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Open data
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Basic information
Entry | Database: PDB / ID: 7mg6 | |||||||||
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Title | Concanavalin A bound to a DNA glycoconjugate, Man-AGCT | |||||||||
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![]() | SUGAR BINDING PROTEIN/DNA / Lectin / DNA complex / 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 | ![]() ![]() synthetic construct (others) | |||||||||
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 | ![]() | 123.5 KB | Display | ![]() |
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PDB format | ![]() | 90.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mg1C ![]() 7mg2C ![]() 7mg3C ![]() 7mg4C ![]() 7mg5C ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 237 / Label seq-ID: 1 - 237
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Components
-Protein / DNA chain / Sugars , 3 types, 6 molecules ABCD![](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 / Source: (natural) ![]() ![]() #2: DNA chain | Mass: 1190.830 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Oligonucleotide conjugated to a mannose residue via a squaramide linker Source: (synth.) synthetic construct (others) #5: Sugar | |
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-Non-polymers , 4 types, 447 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SQ0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SQ0.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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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 (40 uM) and Man-AGCT (160 uM) + 1 uL crystallization condition (Helix screen, condition D3: 0.2 M lithium sulfate, 0.05 M bis Tris (pH 7), 20% ...Details: Sitting drop comprising 1 uL of Concanavalin A (40 uM) and Man-AGCT (160 uM) + 1 uL crystallization condition (Helix screen, condition D3: 0.2 M lithium sulfate, 0.05 M bis Tris (pH 7), 20% v/v MPD). 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: 1.7→70.89 Å / Num. obs: 61815 / % possible obs: 99.6 % / Redundancy: 8.75 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 2.7065 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 9.03 % / Rmerge(I) obs: 0.24 / Num. unique obs: 9422 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JBC Resolution: 1.7→70.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.782 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 25.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→70.89 Å
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Refine LS restraints |
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