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Yorodumi- PDB-1soq: Crystal structure of the transthyretin mutant A108Y/L110E solved ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1soq | ||||||
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Title | Crystal structure of the transthyretin mutant A108Y/L110E solved in space group C2 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hornberg, A. / Olofsson, A. / Eneqvist, T. / Lundgren, E. / Sauer-Eriksson, A.E. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2004 Title: The beta-strand D of transthyretin trapped in two discrete conformations Authors: Hornberg, A. / Olofsson, A. / Eneqvist, T. / 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 | 1soq.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1soq.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 1soq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1soq_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 1soq_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 1soq_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1soq_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/1soq ftp://data.pdbj.org/pub/pdb/validation_reports/so/1soq | HTTPS FTP |
-Related structure data
Related structure data | 1sokSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13885.413 Da / Num. of mol.: 4 / Mutation: A108Y, L110E 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: 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: 2.3 Å3/Da / Density % sol: 46.53 % |
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Crystal grow | Temperature: 291 K / pH: 6 Details: Tris, PEG550MME, ammonium sulfate, sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 29735 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.7 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SOK Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.065 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.201
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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