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- PDB-6tg3: Crystal Structure of the PBP/SBP MotA in complex with glucopinic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tg3 | ||||||
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Title | Crystal Structure of the PBP/SBP MotA in complex with glucopinic acid from A. tumefaciens B6/R10 | ||||||
![]() | MotA | ||||||
![]() | TRANSPORT PROTEIN / solute binding protein / periplasmic binding protein | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / Chem-N7T / MotA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Vigouroux, S. | ||||||
![]() | ![]() Title: Import pathways of the mannityl-opines into the bacterial pathogen Agrobacterium tumefaciens: structural, affinity and in vivo approaches. Authors: Vigouroux, A. / Dore, J. / Marty, L. / Aumont-Nicaise, M. / Legrand, P. / Dessaux, Y. / Vial, L. / Morera, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 513.3 KB | Display | ![]() |
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PDB format | ![]() | 425.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 47.8 KB | Display | |
Data in CIF | ![]() | 67.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tfqC ![]() 6tfsC ![]() 6tfxC ![]() 6tg2C ![]() 5l9gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38455.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-N7T / ( #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4K, 100 mM Tris HCl, 200 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.12 Å / Num. obs: 106626 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Net I/σ(I): 12.42 |
Reflection shell | Resolution: 1.85→1.96 Å / Rmerge(I) obs: 1.143 / Num. unique obs: 16773 / CC1/2: 0.699 / Rpim(I) all: 0.462 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L9G Resolution: 1.85→48.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.115
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Displacement parameters | Biso max: 148.3 Å2 / Biso mean: 45.39 Å2 / Biso min: 16.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→48.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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