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- PDB-6sw4: The structure of AraP, an arabinose binding protein from Geobacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sw4 | ||||||
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Title | The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus | ||||||
![]() | Arabinose binding protein | ||||||
![]() | SUGAR BINDING PROTEIN / Geobacillus stearothermophilus / binding protein / arabinose / three component sensing system | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / Arabinose binding protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lansky, S. / Salama, R. / Lavid, N. / Shoham, Y. / Shoham, G. | ||||||
![]() | ![]() Title: The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus Authors: Lansky, S. / Salama, R. / Lavid, N. / Shoham, Y. / Shoham, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 99.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.8 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g1wS 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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Unit cell |
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Components
#1: Protein | Mass: 37039.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: araP / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 8K, 0.1 M acetate buffer pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 50563 / % possible obs: 99.6 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.84→1.96 Å / Rmerge(I) obs: 1.357 / Num. unique obs: 7925 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3G1W Resolution: 1.845→43.984 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.69 Å2 / Biso mean: 47.0996 Å2 / Biso min: 17.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.845→43.984 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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