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Yorodumi- PDB-1iii: CRYSTAL STRUCTURE OF THE TRANSTHYRETIN MUTANT TTR Y114C-DATA COLL... -
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-Basic information
Entry | Database: PDB / ID: 1iii | ||||||
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Title | CRYSTAL STRUCTURE OF THE TRANSTHYRETIN MUTANT TTR Y114C-DATA COLLECTED AT ROOM TEMPERATURE | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT PROTEIN / GREEK KEY / BETA BARREL | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Eneqvist, T. / Olofsson, A. / Ando, Y. / Lundgren, E. / Sauer-Eriksson, A.E. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Disulfide-Bond Formation in the Transthyretin Mutant Y114C Prevents Amyloid Fibril Formation in Vivo and in Vitro Authors: Eneqvist, T. / Olofsson, A. / Ando, Y. / Miyakawa, T. / Katsuragi, S. / Jass, J. / Lundgren, E. / Sauer-Eriksson, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iii.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iii.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1iii ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1iii | HTTPS FTP |
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-Related structure data
Related structure data | 1iikC 1f41S C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The second part of the biological assembly is generated by the two fold axis: -x, -y, z. |
-Components
#1: Protein | Mass: 13717.329 Da / Num. of mol.: 2 / Fragment: TRANSTHYRETIN / Mutation: Y114C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR / Plasmid: PET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02766 #2: Chemical | ChemComp-BME / #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: 2.24 Å3/Da / Density % sol: 45.04 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2M ammonium sulphate, 0.1M sodium citrate, 2% PEG 200, 1% BME, pH 5.0, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 3, 1998 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 17049 / Num. obs: 17049 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1661 / % possible all: 97.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 155823 |
Reflection shell | *PLUS % possible obs: 97.2 % / Num. unique obs: 1661 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1F41 Resolution: 2→19.54 Å / SU B: 5.509 / SU ML: 0.1578 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2109 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber Details: Occupancy of BME molecules were refined after structural overall B-factor refinement
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Displacement parameters | Biso mean: 19.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.54 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 19.5 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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