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Yorodumi- PDB-6gon: Crystal Structure Of Sea Bream Transthyretin in complex with Perf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gon | ||||||
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Title | Crystal Structure Of Sea Bream Transthyretin in complex with Perfluorooctanoic acid (PFOA). Crystallized in PEG | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / Perfluorooctanoic acid / PFOA | ||||||
Function / homology | Function and homology information thyroid hormone binding / purine nucleobase metabolic process / hormone activity / extracellular space Similarity search - Function | ||||||
Biological species | Sparus aurata (gilthead seabream) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Grundstrom, C. / Zhang, J. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Environ. Sci. Technol. / Year: 2018 Title: Interspecies Variation between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals. Authors: Zhang, J. / Grundstrom, C. / Brannstrom, K. / Iakovleva, I. / Lindberg, M. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E. #1: Journal: Environ. Sci. Technol. / Year: 2016 Title: Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Authors: Zhang, J. / Begum, A. / Brannstrom, K. / Grundstrom, C. / Iakovleva, I. / Olofsson, A. / Sauer-Eriksson, A.E. / Andersson, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gon.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gon.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gon_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6gon_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6gon_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 6gon_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/6gon ftp://data.pdbj.org/pub/pdb/validation_reports/go/6gon | HTTPS FTP |
-Related structure data
Related structure data | 6gnmC 6gnoC 6gnpC 6gnrC 6gnwC 6gooC 6gr7C 6grpC 1sn2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14455.096 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sparus aurata (gilthead seabream) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTT3 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.56 Å3/Da / Density % sol: 51.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. PFOA was added at 5 x molar excess to the protein. The reservoir contained 18% PEG 8K, 0.1M Na ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. PFOA was added at 5 x molar excess to the protein. The reservoir contained 18% PEG 8K, 0.1M Na Cacodylate pH 6.5, 0.2M CaAc. Drop size 3 plus 3 microliter |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→47.1 Å / Num. obs: 71898 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 2 / Num. unique obs: 3605 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1sn2 Resolution: 1.65→43.814 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→43.814 Å
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Refine LS restraints |
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LS refinement shell |
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