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Open data
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Basic information
Entry | Database: PDB / ID: 6bge | ||||||
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Title | HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH 1G2 COMPOUND | ||||||
![]() | VirB11-like protein | ||||||
![]() | ATP binding Protein | ||||||
Function / homology | ![]() secretion by the type IV secretion system / type IV secretion system complex / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arya, T. / Casu, B. / Baron, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CagAlpha in complex with hexamer inhibitor Authors: Arya, T. / Casu, B. / Baron, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.2 KB | Display | ![]() |
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PDB format | ![]() | 110.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.6 KB | Display | ![]() |
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Full document | ![]() | 497.1 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g6oS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 6 - 328 / Label seq-ID: 1 - 323
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36703.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 26 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DN7.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DN7.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-DN7 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis Tris-HCl pH 6.5, 2.0 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→115.44 Å / Num. obs: 18083 / % possible obs: 92.4 % / Redundancy: 5.2 % / Rpim(I) all: 0.08 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.9→3 Å / Num. unique obs: 1737 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G6O Resolution: 2.9→38.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.782 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.33 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→38.53 Å
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Refine LS restraints |
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