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Yorodumi- PDB-2bs8: Crystal structure of F17b-G in complex with N-acetyl-D-glucosamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bs8 | ||||||
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Title | Crystal structure of F17b-G in complex with N-acetyl-D-glucosamine | ||||||
Components | ADHESIN | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / FIMBRIAE / PROTEIN-SUGAR COMPLEX / SUGAR-BINDING PROTEIN | ||||||
Function / homology | Function and homology information adhesion of symbiont to host / pilus / carbohydrate binding / cell adhesion Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Buts, L. / Wellens, A. / VanMolle, I. / Wyns, L. / Loris, R. / Lahmann, M. / Oscarson, S. / DeGreve, H. / Bouckaert, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Impact of Natural Variation in Bacterial F17G Adhesins on Crystallization Behaviour. Authors: Buts, L. / Wellens, A. / Van Molle, I. / Wyns, L. / Loris, R. / Lahmann, M. / Oscarson, S. / De Greve, H. / Bouckaert, J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bs8.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bs8.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/2bs8 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/2bs8 | HTTPS FTP |
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-Related structure data
Related structure data | 1zk5C 1zplC 2bs7C 2bsbC 2bscC 1o9wS C: citing same article (ref.) S: Starting model for refinement |
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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: 18896.871 Da / Num. of mol.: 1 / Fragment: LECTIN DOMAIN, RESIDUES 23-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI B (bacteria) / Description: F17-POSITIVE E. COLI ISOLATE STRAIN / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q47200 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
Sequence details | ELECTRON DENSITY AND NUCLEOTIDE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: HANGING DROP: 1 MICROLITER OF 10% ETHANOL WITH 1.5 M NACL PLUS 1 MICROLITER OF 16 MG/ML F17BG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 2002 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→23 Å / Num. obs: 11000 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O9W Resolution: 2.25→22.91 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2439377.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 216.269 Å2 / ksol: 0.466888 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.35 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→22.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.32 Å / Total num. of bins used: 10 / % reflection obs: 91.1 % |