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Yorodumi- PDB-5f9a: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f9a | ||||||||||||||||||
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Title | Blood group antigen binding adhesin BabA of Helicobacter pylori strain P436 in complex with blood group H Lewis b hexasaccharide | ||||||||||||||||||
Components |
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Keywords | CELL ADHESION / Adhesin / Lectin / Nanobody / Complex | ||||||||||||||||||
Function / homology | Function and homology information SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||||||||||||||
Biological species | Helicobacter pylori (bacteria) Lama glama (llama) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||||||||||||||
Authors | Moonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H. | ||||||||||||||||||
Funding support | Belgium, Sweden, 5items
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Citation | Journal: Cell Host Microbe / Year: 2016 Title: Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori. Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / ...Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / Coppens, F. / Lo, A.W. / Ny, T. / Solnick, J.V. / Vandenbussche, G. / Oscarson, S. / Hammarstrom, L. / Arnqvist, A. / Berg, D.E. / Muyldermans, S. / Boren, T. / Remaut, H. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f9a.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f9a.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 5f9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9a ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9a | HTTPS FTP |
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-Related structure data
Related structure data | 5f7kSC 5f7lC 5f7mC 5f7nC 5f7wC 5f7yC 5f8qC 5f8rC 5f93C 5f97C 5f9dC 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: 48900.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: In this hybrid construct the insertion domain of the Peruvian strain P436 (residues 179 to 258, responsible for carbohydrate binding) was grafted into the framework of the generalist strain 17875 Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2, babA / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: O52269, UniProt: Q6DT10 |
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#2: Antibody | Mass: 13260.856 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): WK6 |
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M Sodium acetate, 100 mM Imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→51.54 Å / Num. obs: 39582 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.44→2.57 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F7K Resolution: 2.44→51.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.014 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.443 Å2
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Refinement step | Cycle: 1 / Resolution: 2.44→51.54 Å
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Refine LS restraints |
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