+Open data
-Basic information
Entry | Database: PDB / ID: 6avz | ||||||
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Title | Crystal structure of the HopQ-CEACAM3 WT complex | ||||||
Components |
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Keywords | CELL ADHESION | ||||||
Function / homology | Function and homology information regulation of immune system process / specific granule membrane / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / Neutrophil degranulation / cell surface / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) Homo sapiens (human) Helicobacter pylori P12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Bonsor, D.A. / Sundberg, E.J. | ||||||
Citation | Journal: EMBO J. / Year: 2018 Title: TheHelicobacter pyloriadhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA. Authors: Bonsor, D.A. / Zhao, Q. / Schmidinger, B. / Weiss, E. / Wang, J. / Deredge, D. / Beadenkopf, R. / Dow, B. / Fischer, W. / Beckett, D. / Wintrode, P.L. / Haas, R. / Sundberg, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6avz.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6avz.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 6avz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/6avz ftp://data.pdbj.org/pub/pdb/validation_reports/av/6avz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47027.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: hopQ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H6A3H4 | ||
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#2: Protein | Mass: 12045.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM3, CD66D, CGM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40198 | ||
#3: Protein/peptide | Mass: 273.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori P12 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) | ||
#4: Chemical | #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: 1.94 Å3/Da / Density % sol: 36.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% w/v PEG 3000, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M calcium acetate, 1 % v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2017 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→103.26 Å / Num. obs: 29535 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rpim(I) all: 0.043 / Rsym value: 0.054 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2202 / Rpim(I) all: 0.719 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→103.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.543 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.358 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→103.26 Å
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Refine LS restraints |
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