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- PDB-5l9o: Crystal structure of Agrobacterium tumefaciens C58 strain PBP Soc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l9o | ||||||
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Title | Crystal structure of Agrobacterium tumefaciens C58 strain PBP SocA in complex with glucopine | ||||||
![]() | Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein | ||||||
![]() | TRANSPORT PROTEIN / periplasmic binding protein / ABC transporter / synthetic opine | ||||||
Function / homology | ![]() ligand-gated monoatomic ion channel activity / periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marty, L. / Morera, S. | ||||||
![]() | ![]() Title: Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens. Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / 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 | ![]() | 203.9 KB | Display | ![]() |
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PDB format | ![]() | 163.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l9gC ![]() 5l9iC ![]() 5l9lC ![]() 5l9pC ![]() 5l9sC ![]() 5lomC ![]() 6hqhC ![]() 4ymxS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28879.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: socA, Atu5006 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 36% PEG 4K, 0.1 M HEPES pH 7.5 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2014 |
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: 33762 / % possible obs: 96.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.16 Å2 / Rsym value: 0.072 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 1.84→1.9 Å / Rsym value: 0.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YMX Resolution: 1.84→33.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.16
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Displacement parameters | Biso mean: 42.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.84→33.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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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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