+Open data
-Basic information
Entry | Database: PDB / ID: 1ijn | ||||||
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Title | Crystal structure of the transthyretin mutant TTR C10A/Y114C | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT PROTEIN / GREEK KEY / BETA BARREL | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Eneqvist, T. / Karlsson, A. / Olofsson, A. / Sauer-Eriksson, A.E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Cys114-linked dimers of transthyretin are compatible with amyloid formation Authors: Karlsson, A. / Olofsson, A. / Eneqvist, T. / Sauer-Eriksson, A.E. #1: 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 | 1ijn.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ijn.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ijn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ijn_validation.pdf.gz | 386.5 KB | Display | wwPDB validaton report |
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Full document | 1ijn_full_validation.pdf.gz | 388.8 KB | Display | |
Data in XML | 1ijn_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1ijn_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ijn ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ijn | HTTPS FTP |
-Related structure data
Related structure data | 1f41S 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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2 |
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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: 13685.265 Da / Num. of mol.: 2 / Fragment: TRANSTHYRETIN / Mutation: C10A/Y114C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / 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: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 40% PEG 550 monomethyl ether, 0.1M sodium citrate, 0.1M ammonium sulphate, 0.1% BME, pH 5.0, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 31, 2000 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 26695 / Num. obs: 26695 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2479 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1F41 Resolution: 1.7→19.92 Å / SU B: 3.46166 / SU ML: 0.1173 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12929 / ESU R Free: 0.1222 / 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: 19.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.92 Å
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Refine LS restraints |
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