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- PDB-6x3q: Hsa Siglec and Unique domains in complex with 3'sialyl-N-acetylla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x3q | ||||||||||||
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Title | Hsa Siglec and Unique domains in complex with 3'sialyl-N-acetyllactosamine trisaccharide | ||||||||||||
![]() | Streptococcal hemagglutinin | ||||||||||||
![]() | CELL ADHESION / adhesin / serine rich repeat adhesin / bacterial adhesion / protein | ||||||||||||
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 | ![]() | 101.2 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 794.9 KB | Display | ![]() |
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Full document | ![]() | 799.9 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ef7C ![]() 6ef9C ![]() 6efaC ![]() 6efbC ![]() 6efcSC ![]() 6efdC ![]() 6effC ![]() 6efiC ![]() 6x3kC ![]() 7kmjC S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 25837.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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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: 1.94 Å3/Da / Density % sol: 36.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 21.6 mg/mL protein in 20 mM Tris-HCl, pH 7.2 sitting drop vapor diffusion drops contain 1uL protein solution and 2uL reservoir solution. Reservoir solution: 0.1 M Succinate/Phosphate/Glycine ...Details: 21.6 mg/mL protein in 20 mM Tris-HCl, pH 7.2 sitting drop vapor diffusion drops contain 1uL protein solution and 2uL reservoir solution. Reservoir solution: 0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350. Crystals were soaked with 5mM ligand for 20 hours, no cryoprotection was used beyond the reservoir buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 10881 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 34.14 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.055 / Rsym value: 0.126 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.15→2.19 Å / Num. unique obs: 539 / Rpim(I) all: 0.283 / Rsym value: 0.643 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EFC Resolution: 2.15→32.42 Å / SU ML: 0.2679 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9891 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: 44.6 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→32.42 Å
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Refine LS restraints |
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LS refinement shell |
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