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Open data
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Basic information
Entry | Database: PDB / ID: 7ndr | ||||||
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Title | Crystal structure of TphC in an open conformation | ||||||
![]() | Tripartite tricarboxylate transporter substrate binding protein | ||||||
![]() | TRANSPORT PROTEIN / Solute binding protein | ||||||
Function / homology | Bordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / periplasmic space / Tripartite tricarboxylate transporter substrate binding protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Levy, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of terephthalate recognition by solute binding protein TphC. Authors: Gautom, T. / Dheeman, D. / Levy, C. / Butterfield, T. / Alvarez Gonzalez, G. / Le Roy, P. / Caiger, L. / Fisher, K. / Johannissen, L. / Dixon, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 812.1 KB | Display | ![]() |
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PDB format | ![]() | 546.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.6 KB | Display | ![]() |
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Full document | ![]() | 478.9 KB | Display | |
Data in XML | ![]() | 75.5 KB | Display | |
Data in CIF | ![]() | 112.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ndsC ![]() 4x9tS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 33792.711 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus B5 - 0.09M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide) 0.1M Buffer System 2 pH 7.5 (1.0M 7.5 Sodium HEPES; MOPS (acid) ) 30% v/v precipitant mix 1 (40% ...Details: Morpheus B5 - 0.09M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide) 0.1M Buffer System 2 pH 7.5 (1.0M 7.5 Sodium HEPES; MOPS (acid) ) 30% v/v precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→70.48 Å / Num. obs: 161975 / % possible obs: 99.41 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.13 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2251 / Rpim(I) all: 0.0927 / Rrim(I) all: 0.2438 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.88→1.947 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.175 / Mean I/σ(I) obs: 0.56 / Num. unique obs: 16108 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.88 / Rrim(I) all: 2.35 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4X9T Resolution: 1.97→70.48 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5947 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→70.48 Å
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Refine LS restraints |
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LS refinement shell |
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