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- PDB-4qrf: Crystal structure of V30M mutant human transthyretin complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qrf | ||||||
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Title | Crystal structure of V30M mutant human transthyretin complexed with caffeic acid phenethyl ester | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / transporter / thyroxine binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yokoyama, T. / Kosaka, Y. / Mizuguchi, M. | ||||||
![]() | ![]() Title: Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin Authors: Yokoyama, T. / Kosaka, Y. / Mizuguchi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61 KB | Display | ![]() |
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PDB format | ![]() | 43.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 959.6 KB | Display | ![]() |
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Full document | ![]() | 961.7 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pweC ![]() 4pwfC ![]() 4pwgC ![]() 4pwhC ![]() 4pwiC ![]() 4pwjC ![]() 4pwkC ![]() 4pewS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10-30% PEG400, 0.1M HEPES, 0.2M CaCl2, 1mM caffeic acid phenethyl ester, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 13, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 22978 / Num. obs: 22978 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 26.39 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1082 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PEW Resolution: 1.8→32.888 Å / FOM work R set: 0.812 / SU ML: 0.25 / σ(F): 1.38 / Phase error: 25.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.16 Å2 / Biso mean: 25.38 Å2 / Biso min: 8.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→32.888 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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