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Yorodumi- PDB-5ok8: Crystal structure of protein Lpp20 (HP1456) from Helicobacter pylori -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ok8 | ||||||
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Title | Crystal structure of protein Lpp20 (HP1456) from Helicobacter pylori | ||||||
Components | LPP20 lipoprotein | ||||||
Keywords | UNKNOWN FUNCTION / Virulence factor / Helicobacter pylori / Lipoprotein | ||||||
Function / homology | Lipoprotein LPP20 / Lipoprotein LPP20-like / LPP20 lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / LPP20 lipoprotein Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.874 Å | ||||||
Authors | Zanotti, G. / Mishra, N. / Valesse, F. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: Helicobacter pylori antigenic Lpp20 is a structural homologue of Tip alpha and promotes epithelial-mesenchymal transition. Authors: Vallese, F. / Mishra, N.M. / Pagliari, M. / Berto, P. / Codolo, G. / de Bernard, M. / Zanotti, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ok8.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ok8.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ok8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/5ok8 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5ok8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19140.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain J99 / ATCC 700824) (bacteria) Gene: lpp20, jhp_1349 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A0V1 #2: Chemical | ChemComp-EPE / | #3: Chemical | ChemComp-CA / | #4: 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: 2.83 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 20% PEG 6000 (solution number 44 of PEGS-II Suit screen, Quiagen, Germany) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→48.38 Å / Num. obs: 87448 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.018 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.86→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.992 / Rpim(I) all: 0.471 / % possible all: 89.9 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.874→48.377 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 31.57 / 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: 1.874→48.377 Å
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Refine LS restraints |
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LS refinement shell |
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