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- PDB-1qfo: N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH 3'SIALY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qfo | |||||||||
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Title | N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH 3'SIALYLLACTOSE | |||||||||
![]() | PROTEIN (SIALOADHESIN) | |||||||||
![]() | IMMUNE SYSTEM / IMMUNOGLOBULIN SUPERFAMILY / CARBOHYDRATE BINDING | |||||||||
Function / homology | ![]() positive regulation of T cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / virion binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | May, A.P. / Robinson, R.C. / Vinson, M. / Crocker, P.R. / Jones, E.Y. | |||||||||
![]() | ![]() Title: Crystal structure of the N-terminal domain of sialoadhesin in complex with 3' sialyllactose at 1.85 A resolution. Authors: May, A.P. / Robinson, R.C. / Vinson, M. / Crocker, P.R. / Jones, E.Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 13319.107 Da / Num. of mol.: 3 / Fragment: N-TERMINAL SIALIC ACID-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | #3: Sugar | ChemComp-SIA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 30 % (W/V) PEG 4000, 10 MM DTT, 0.1M SODIUM HEPES PH 5.6, 5MG/ML PROTEIN, 12.5MM 3'SIALYLLACTOSE | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 33750 / Num. obs: 33750 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.85→1.97 Å / % possible all: 84.24 |
Reflection shell | *PLUS % possible obs: 84.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: N-TERMINAL DOMAIN OF SIALOADHESIN Resolution: 1.85→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 3314732.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.52 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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