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Yorodumi- PDB-3ozk: Crystal structure of human transthyretin variant A25T in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ozk | |||||||||
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Title | Crystal structure of human transthyretin variant A25T in complex with thyroxine (T4) | |||||||||
Components | Transthyretin | |||||||||
Keywords | HORMONE / T4 transport / Retinol binding protein | |||||||||
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 / Resolution: 1.9 Å | |||||||||
Authors | Lima, L.M.T.R. / Palmieri, L.C. / Foguel, D. / Palhano, F.L. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of human transthyretin variant A25T in complex with thyroxine (T4) Authors: Lima, L.M.T.R. / Palmieri, L.C. / Foguel, D. / Palhano, F.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ozk.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ozk.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ozk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/3ozk ftp://data.pdbj.org/pub/pdb/validation_reports/oz/3ozk | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13807.387 Da / Num. of mol.: 2 / Mutation: A25T 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: 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: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes sodium pH 7.5, 28% PEG 400, 0.2 calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, complex obtained by soaking crystal with ligand. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.1 % / Av σ(I) over netI: 7.4 / Number: 79832 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / D res high: 1.9 Å / D res low: 64.34 Å / Num. obs: 19350 / % possible obs: 99.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.9→64.34 Å / Num. all: 19350 / Num. obs: 19350 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 17.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.9→26.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.425 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→26.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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