+Open data
-Basic information
Entry | Database: PDB / ID: 6efi | ||||||
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Title | SK678 binding region (Siglec + Unique) | ||||||
Components | KxYKxGKxW signal domain protein | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sanguinis SK678 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.715 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 | 6efi.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6efi.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 6efi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/6efi ftp://data.pdbj.org/pub/pdb/validation_reports/ef/6efi | HTTPS FTP |
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-Related structure data
Related structure data | 6ef7C 6ef9C 6efaC 6efbC 6efcC 6efdC 6effC 6x3kC 6x3qC 7kmjC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/510 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23185.537 Da / Num. of mol.: 2 / Fragment: residues 251-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sanguinis SK678 (bacteria) Gene: srpA, HMPREF9392_0959 / Production host: Escherichia coli (E. coli) / References: UniProt: F0FS71 |
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-Non-polymers , 5 types, 537 molecules
#2: Chemical | #3: Chemical | ChemComp-CO / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M bicine pH 7.6, 25% PEG 6000, 0.005 M hexamine Cobalt chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 45715 / % possible obs: 97.7 % / Redundancy: 7 % / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.7→1.74 Å |
-Processing
Software | Name: PHENIX / Version: (1.12_2829) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.715→38.718 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.62 / 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: 1.715→38.718 Å
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Refine LS restraints |
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LS refinement shell |
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