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- PDB-8i7q: Cobalt and Calcium coordinated Concanavalin A at pH 7.4 from Cana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i7q | |||||||||
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Title | Cobalt and Calcium coordinated Concanavalin A at pH 7.4 from Canavalia ensiformis | |||||||||
![]() | Concanavalin A | |||||||||
![]() | SUGAR BINDING PROTEIN / lectin | |||||||||
Function / homology | : ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hwang, Y. / Jeong, J.H. / Lee, S.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Selective interactions of Co 2+ -Ca 2+ -concanavalin A with high mannose N -glycans. Authors: Hwang, Y. / Jeong, J.H. / Lee, D.H. / Lee, S.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 | ![]() | 58.7 KB | Display | ![]() |
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PDB format | ![]() | 40.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 960.4 KB | Display | ![]() |
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Full document | ![]() | 961.8 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 25592.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.51 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.01 M cobalt(II) chloride hexahydrate, 0.1 M MES monohydrate pH 6.5, 1.8 M ammonium sulfate |
-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: May 2, 2022 / Details: In-vacuum Undulator |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→27.93 Å / Num. obs: 5904 / % possible obs: 99.9 % / Redundancy: 2 % / Rrim(I) all: 0.0702 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.83→2.93 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 588 / Rrim(I) all: 0.413 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→27.93 Å
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Refine LS restraints |
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LS refinement shell |
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