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Yorodumi- PDB-4zh7: Structural basis of Lewisb antigen binding by the Helicobacter py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zh7 | |||||||||
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Title | Structural basis of Lewisb antigen binding by the Helicobacter pylori adhesin BabA | |||||||||
Components | Outer membrane protein-adhesin | |||||||||
Keywords | SUGAR BINDING PROTEIN / blood group antigen binding / adhesin / Lewisb | |||||||||
Function / homology | SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane protein-adhesin Function and homology information | |||||||||
Biological species | Helicobacter pylori (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | |||||||||
Authors | Howard, T. / Hage, N. / Phillips, C. / Brassington, C.A. / Debreczeni, J. / Overman, R. / Gellert, P. / Stolnik, S. / Winkler, G.S. / Falcone, F.H. | |||||||||
Citation | Journal: Sci Adv / Year: 2015 Title: Structural basis of Lewis(b) antigen binding by the Helicobacter pylori adhesin BabA. Authors: Hage, N. / Howard, T. / Phillips, C. / Brassington, C. / Overman, R. / Debreczeni, J. / Gellert, P. / Stolnik, S. / Winkler, G.S. / Falcone, F.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zh7.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zh7.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zh7 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zh7 | HTTPS FTP |
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-Related structure data
Related structure data | 4zh0C 4zhoS 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: 58251.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA, jhp_0833 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZKV2 |
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#2: 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 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 22% PEG 3350, 0.1 M PCTP (pH = 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→44.78 Å / Num. obs: 29319 / % possible obs: 98.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.643 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZHO Resolution: 2.12→44.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.047 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.175 / 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: 27.888 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→44.78 Å
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Refine LS restraints |
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