+Open data
-Basic information
Entry | Database: PDB / ID: 7nr2 | ||||||
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Title | The structure of the SBP TarP_Sse in complex with coumarate | ||||||
Components | TRAP dicarboxylate transporter, DctP subunit | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein / TRAP transporter / solute binding protein / hydroxycinnamate | ||||||
Function / homology | TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / : / transmembrane transport / periplasmic space / 4'-HYDROXYCINNAMIC ACID / TRAP dicarboxylate transporter, DctP subunit Function and homology information | ||||||
Biological species | Sagittula stellata E-37 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.13 Å | ||||||
Authors | 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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Citation | Journal: Febs J. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nr2.cif.gz | 490 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nr2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/7nr2 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/7nr2 | HTTPS FTP |
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-Related structure data
Related structure data | 7nqgC 7nraC 7nrrC 7nswC 7ntdC 7nteC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37549.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SeMet derivative. C-terminal linker and 6xHIS tag, not visible in structure. Source: (gene. exp.) Sagittula stellata E-37 (bacteria) / Gene: SSE37_24379 / Production host: Escherichia coli (E. coli) / References: UniProt: A3K0X1 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HC4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 0.2 M NaCl, 0.1 M sodium cacodylate pH 6.25 and 1.8 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97918, 0.97938 | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.13→50.5 Å / Num. obs: 77509 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.062 / Net I/σ(I): 12.5 | |||||||||
Reflection shell | Resolution: 2.13→2.19 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5746 / Rpim(I) all: 0.343 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.13→50.496 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.078 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.222 / ESU R Free: 0.193 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.713 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→50.496 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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