+Open data
-Basic information
Entry | Database: PDB / ID: 6efb | ||||||
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Title | GspB Siglec domain | ||||||
Components | SK150 siglec + Unique | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin | ||||||
Function / homology | Immunoglobulin-like - #4140 / Ubiquitin-like (UB roll) - #890 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Function and homology information | ||||||
Biological species | Streptococcus gordonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Iverson, T.M. | ||||||
Funding support | United States, 1items
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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 | 6efb.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6efb.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 6efb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6efb_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 6efb_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 6efb_validation.xml.gz | 11 KB | Display | |
Data in CIF | 6efb_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/6efb ftp://data.pdbj.org/pub/pdb/validation_reports/ef/6efb | HTTPS FTP |
-Related structure data
Related structure data | 6ef7C 6ef9C 6efaC 6efcC 6efdC 6effC 6efiC 6x3kC 6x3qC 7kmjC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/508 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23518.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus gordonii (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonim sulfate, 25% PEG 4000, 15% ethanol. 0.1 M Bis-tris pH 7.0 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.542 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Oct 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 14767 / % possible obs: 97.3 % / Redundancy: 9 % / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.9→1.94 Å |
-Processing
Software | Name: PHENIX / Version: (1.11.1_2575) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→23.606 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.26 / Stereochemistry target values: ML
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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: 1.9→23.606 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.9764 Å / Origin y: -0.8306 Å / Origin z: 14.5766 Å
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Refinement TLS group | Selection details: all |