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Yorodumi- PDB-5l4f: Crystal Structure of Human Transthyretin in Complex with 2,6-Dini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l4f | ||||||
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Title | Crystal Structure of Human Transthyretin in Complex with 2,6-Dinitro-p-cresol (DNPC) | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / thyroxine binding / 2 / 6-Dinitro-p-cresol (DNPC)complex | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Grundstrom, C. / Hall, M. / Zhang, J. / Olofsson, A. / Andersson, P. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | 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 | 5l4f.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l4f.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 5l4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/5l4f ftp://data.pdbj.org/pub/pdb/validation_reports/l4/5l4f | HTTPS FTP |
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-Related structure data
Related structure data | 5jidC 5jimC 5jiqC 5l4iC 5l4jC 5l4mC 1f41S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: 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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. DNPC was added at 5 x molar excess to the protein. The reservoir ...Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. DNPC was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent glycerol at pH 5.5. Drop size 3 plus 3 microliter |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→42.9 Å / Num. obs: 40934 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F41 Resolution: 1.48→42.855 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→42.855 Å
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Refine LS restraints |
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LS refinement shell |
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