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- PDB-1qgl: Room temperature structure of concanavalin A complexed to bivalen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qgl | ||||||
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Title | Room temperature structure of concanavalin A complexed to bivalent ligand | ||||||
![]() | PROTEIN (SUCCINYLATED CONCANAVALIN A ) | ||||||
![]() | LECTIN (AGGLUTININ) / CONCANAVLIN A / SACCHARIDE BINDING / RECOGNITION COMPLEX | ||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Naismith, J.H. | ||||||
![]() | Journal: J.Am.Chem.Soc. / Year: 1999 Title: On the Meaning of Affinity: Cluster Glycoside Effects and Concanavalin A Authors: Dimick, S.M. / Powell, S.C. / Mcmahon, S.A. / Moothoo, D.N. / Naismith, J.H. / Toone, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 732 KB | Display | ![]() |
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Full document | ![]() | 737.6 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cnaS 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 oper: (Code: given Matrix: (-0.68145, -0.00034, 0.73186), Vector: |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/EJT.gif)
![](data/chem/img/EJT.gif)
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COMPLEXED WITH BIVALENT LIGAND / Source: (natural) ![]() ![]() #4: Sugar | ChemComp-EJT / | |
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-Non-polymers , 4 types, 77 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-SIN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293.5 K / pH: 7 / Method: vapor diffusion, sitting drop / Details: Moothoo, D.N., (1998) Acta Crystallogr, D54, 1023. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: NONIUS / Detector: IMAGE PLATE / Details: MIRROR |
Radiation | Monochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→26 Å / Num. obs: 21164 / % possible obs: 96.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 |
Reflection | *PLUS Lowest resolution: 26 Å / Num. obs: 21182 / % possible obs: 96.4 % |
Reflection shell | *PLUS Highest resolution: 2.66 Å / Lowest resolution: 2.75 Å / % possible obs: 98.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.207 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CNA Resolution: 2.66→26 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2919789.43 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: CNS DEFAULT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.66→26 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.66→2.83 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 26 Å / % reflection Rfree: 10 % / Rfactor obs: 0.176 / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.257 / Rfactor obs: 0.239 |