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- PDB-7vev: Crystal structure of bacterial chemotaxis-dependent pectin-bindin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vev | ||||||
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Title | Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES | ||||||
![]() | SPH1118 | ||||||
![]() | SUGAR BINDING PROTEIN / pectin-binding protein / chemotaxis / gram-negative bacteria | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Anamizu, K. / Takase, R. / Hio, M. / Watanebe, D. / Mikami, B. / Hashimoto, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation. Authors: Anamizu, K. / Takase, R. / Hio, M. / Watanabe, D. / Mikami, B. / Hashimoto, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.9 KB | Display | ![]() |
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PDB format | ![]() | 113 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 969.3 KB | Display | ![]() |
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Full document | ![]() | 972 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7veqC ![]() 7verC ![]() 7vetC ![]() 7veuC ![]() 7vewC ![]() 5ipwS C: citing same article ( S: Starting model for refinement |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 70050.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG6000 0.2 M Calcium chloride 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→50 Å / Num. obs: 79704 / % possible obs: 99.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.5→1.52 Å / Rmerge(I) obs: 0.139 / Num. unique obs: 10578 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IPW Resolution: 1.498→26.133 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.078 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.403 Å2
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Refinement step | Cycle: LAST / Resolution: 1.498→26.133 Å
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Refine LS restraints |
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LS refinement shell |
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