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Open data
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Basic information
Entry | Database: PDB / ID: 5t4y | ||||||
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Title | Crystal structure of BT1762-1763 | ||||||
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![]() | TRANSPORT PROTEIN / outer membrane protein / protein complex / TonB dependent transporter / carbohydrate binding protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den Berg, B. | ||||||
![]() | ![]() Title: Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Authors: Glenwright, A.J. / Pothula, K.R. / Bhamidimarri, S.P. / Chorev, D.S. / Basle, A. / Firbank, S.J. / Zheng, H. / Robinson, C.V. / Winterhalter, M. / Kleinekathofer, U. / Bolam, D.N. / van den Berg, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 909.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468 KB | Display | ![]() |
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Full document | ![]() | 519.2 KB | Display | |
Data in XML | ![]() | 94.1 KB | Display | |
Data in CIF | ![]() | 127.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fq3C ![]() 5fq4C ![]() 5fq6C ![]() 5fq7C ![]() 5fq8C ![]() 5lx8C ![]() 5t3rSC 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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Unit cell |
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Components
#1: Protein | Mass: 65858.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q8A6W4 #2: Protein | Mass: 115483.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q8A6W3 #3: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18-20% PEG3350 50 mM Hepes pH 7.0 0.2 M NH4NO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→130.46 Å / Num. obs: 86975 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3 |
Reflection shell | Highest resolution: 2.99 Å / Rmerge(I) obs: 1.17 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5T3R Resolution: 3.1→130.348 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→130.348 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.138 Å / Rfactor Rfree: 0.467 / Rfactor Rwork: 0.385 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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