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Yorodumi- PDB-6x3q: Hsa Siglec and Unique domains in complex with 3'sialyl-N-acetylla... -
+Open data
-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 | ||||||||||||
Components | Streptococcal hemagglutinin | ||||||||||||
Keywords | CELL ADHESION / adhesin / serine rich repeat adhesin / bacterial adhesion / protein | ||||||||||||
Function / homology | Function and homology information surface biofilm formation / biofilm matrix assembly / cell adhesion / extracellular region Similarity search - Function | ||||||||||||
Biological species | Streptococcus gordonii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||||||||
Authors | Stubbs, H.E. / Iverson, T.M. | ||||||||||||
Funding support | 3items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x3q.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x3q.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 6x3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/6x3q ftp://data.pdbj.org/pub/pdb/validation_reports/x3/6x3q | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptococcus gordonii (bacteria) / Strain: Challis / Gene: hsa, SGO_0966 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AWU7 | ||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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