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Yorodumi- PDB-6gnm: Crystal Structure Of Sea Bream Transthyretin in complex with 2,2'... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gnm | ||||||
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Title | Crystal Structure Of Sea Bream Transthyretin in complex with 2,2',4,4'-tetrahydroxybenzophenone (BP2) | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / thyroxine disrupting chemicals / TDCs / 2 / 2' / 4 / 4'-tetrahydroxybenzophenone / BP2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sparus aurata (gilthead seabream) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 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 | 6gnm.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gnm.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 6gnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/6gnm ftp://data.pdbj.org/pub/pdb/validation_reports/gn/6gnm | HTTPS FTP |
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-Related structure data
Related structure data | 6gnoC 6gnpC 6gnrC 6gnwC 6gonC 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: 2.52 Å3/Da / Density % sol: 51.24 % |
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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. BP2 was added at 5 x molar excess to the protein. The reservoir contained 0.01M ZnSO4 hepahyrate, 0. ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. BP2 was added at 5 x molar excess to the protein. The reservoir contained 0.01M ZnSO4 hepahyrate, 0.1M MES pH 6.5, 25% PEG-MME 550. Drop size 3 plus 3 microliter |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→59.56 Å / Num. obs: 27586 / % possible obs: 95.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.24→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.3 / % possible all: 81.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SN2 Resolution: 2.24→59.56 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→59.56 Å
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Refine LS restraints |
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LS refinement shell |
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