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Open data
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Basic information
Entry | Database: PDB / ID: 7kmj | ||||||||||||
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Title | Hsa Siglec and Unique domains in complex with Sialyl Lewis C | ||||||||||||
![]() | Streptococcal hemagglutinin | ||||||||||||
![]() | CELL ADHESION / adhesin | ||||||||||||
Function / homology | ![]() surface biofilm formation / biofilm matrix assembly / cell adhesion / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Stubbs, H.E. / Iverson, T.M. | ||||||||||||
Funding support | 3items
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![]() | ![]() Title: Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation. Authors: Bensing, B.A. / Stubbs, H.E. / Agarwal, R. / Yamakawa, I. / Luong, K. / Solakyildirim, K. / Yu, H. / Hadadianpour, A. / Castro, M.A. / Fialkowski, K.P. / Morrison, K.M. / Wawrzak, Z. / Chen, ...Authors: Bensing, B.A. / Stubbs, H.E. / Agarwal, R. / Yamakawa, I. / Luong, K. / Solakyildirim, K. / Yu, H. / Hadadianpour, A. / Castro, M.A. / Fialkowski, K.P. / Morrison, K.M. / Wawrzak, Z. / Chen, X. / Lebrilla, C.B. / Baudry, J. / Smith, J.C. / Sullam, P.M. / Iverson, T.M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.4 KB | Display | ![]() |
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PDB format | ![]() | 108.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ef7C ![]() 6ef9C ![]() 6efaC ![]() 6efbC ![]() 6efcC ![]() 6efdC ![]() 6effC ![]() 6efiC ![]() 6x3kC ![]() 6x3qC ![]() 5eq2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25837.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Challis / Gene: hsa, SGO_0966 / Production host: ![]() ![]() | ||||
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 21.6 mg/ml in 20 mM Tris-HCl, pH 7.2. Equilibrate 1 ul protein and 2 ul reservoir solution over 50 ul of reservoir solution (0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350). ...Details: 21.6 mg/ml in 20 mM Tris-HCl, pH 7.2. Equilibrate 1 ul protein and 2 ul reservoir solution over 50 ul of reservoir solution (0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350). Crystals were soaked in reservoir solution supplemented with 5 mM of sLec for 20 hr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 1748709 / % possible obs: 99.7 % / Redundancy: 8 % / Biso Wilson estimate: 16.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Num. unique obs: 2468 / CC1/2: 0.891 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EQ2 Resolution: 1.33→37.99 Å / SU ML: 0.1624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6886 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→37.99 Å
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Refine LS restraints |
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LS refinement shell |
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