+Open data
-Basic information
Entry | Database: PDB / ID: 3dk0 | ||||||
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Title | Crystal structure of transthyretin variant L55P at acidic pH | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / TTR / AMYLOID FIBRILS / POINT MUTATION / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Cendron, L. / Zanotti, G. / Folli, C. / Berni, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses. Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / Berni, R. #1: Journal: J.Mol.Biol. / Year: 2007 Title: Acidic Ph-Induced Conformational Changes in Amyloidogenic Mutant Transthyretin. Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G. #2: Journal: J.Mol.Biol. / Year: 2000 Title: A Comparative Analysis of 23 Structures of the Amyloidogenic Protein Transthyretin. Authors: Eneqvist, T. / Olofsson, A. / 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 | 3dk0.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dk0.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dk0 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dk0 | HTTPS FTP |
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-Related structure data
Related structure data | 3djrC 3djsC 3djtC 3djzC 3dk2C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13761.317 Da / Num. of mol.: 2 / Mutation: L55P Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / 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: 2.15 Å3/Da / Density % sol: 42.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.6 Details: 32% PEG 400, 0.05-0.2M CaCl2, 0.1M NaHepes , pH 4.6, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→51.3 Å / Num. all: 19735 / Num. obs: 19735 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2554 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F41 Resolution: 1.87→42.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.171 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.867 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→42.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.867→1.916 Å / Total num. of bins used: 20
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