+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ntd | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of the SBP TarP_Csal in complex with ferulate | ||||||
![]() | TRAP dicarboxylate transporter-DctP subunit | ||||||
![]() | TRANSPORT PROTEIN / TRAP transporter / solute binding protein / periplasmic / hydroxycinnamate / lignin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: The structural basis for high-affinity uptake of lignin-derived aromatic compounds by proteobacterial TRAP transporters. Authors: Bisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 154.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7nqgC ![]() 7nr2C ![]() 7nraC ![]() 7nrrC ![]() 7nswSC ![]() 7nteC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37303.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal 6xHis tag and linker Source: (gene. exp.) ![]() Strain: ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11 Gene: Csal_0280 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.44 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5 and 20 % (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.89 Å / Num. obs: 62516 / % possible obs: 96.8 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.073 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.687 / Num. unique obs: 4572 / CC1/2: 0.47 / Rpim(I) all: 0.62 / % possible all: 95.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7NSW Resolution: 1.75→47.124 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.876 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.138 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.081 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.124 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|