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Open data
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Basic information
Entry | Database: PDB / ID: 7nte | ||||||
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Title | The structure of an open conformation of the SBP TarP_Csal | ||||||
![]() | TRAP dicarboxylate transporter-DctP subunit | ||||||
![]() | TRANSPORT PROTEIN / TRAP transporter / solute binding protein / periplasmic / hydroxycinnamate / lignin | ||||||
Function / homology | TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / : / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / transmembrane transport / metal ion binding / TRAP dicarboxylate transporter-DctP subunit![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J. | ||||||
Funding support | 1items
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.6 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7nqgC ![]() 7nr2C ![]() 7nraC ![]() 7nrrC ![]() 7nswC ![]() 7ntdSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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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: 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: 1.95 Å3/Da / Density % sol: 36.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M MgCl2, 0.1 M Hepes pH 7.0 and 25 % (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→53.43 Å / Num. obs: 74222 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.038 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.603 / Num. unique obs: 5395 / CC1/2: 0.717 / Rpim(I) all: 0.379 / Rrim(I) all: 0.715 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NTD Resolution: 1.6→53.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.91 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200 Å2 / Biso mean: 22.754 Å2 / Biso min: 6.85 Å2
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Refinement step | Cycle: final / Resolution: 1.6→53.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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