+
Open data
-
Basic information
Entry | Database: PDB / ID: 7mgd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Concanavalin A bound to a DNA glycoconjugate, T(Man-T)TT | |||||||||
![]() | 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 | ![]()
| |||||||||
![]() | ![]() Title: Redefining Protein Interfaces within Protein Single Crystals with DNA. Authors: Partridge, B.E. / Winegar, P.H. / Han, Z. / Mirkin, C.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 198.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 156.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466.1 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mg1C ![]() 7mg2C ![]() 7mg3C ![]() 7mg4C ![]() 7mg5C ![]() 7mg6C ![]() 7mg7C ![]() 7mg8C ![]() 7mg9C ![]() 7mgaC ![]() 7mgbC ![]() 7mgcC ![]() 1jbcS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / 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
NCS ensembles :
|
-
Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-CA / #4: Sugar | ChemComp-MMA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and T(Man-T)TT (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium chloride ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and T(Man-T)TT (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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→60.53 Å / Num. obs: 52751 / % possible obs: 91.5 % / Redundancy: 2.48 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 3.2777 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.33 / Num. unique obs: 7339 / % possible all: 83.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1JBC Resolution: 2.05→60.53 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.144 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 32.32 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→60.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|