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Yorodumi- PDB-4y9c: Crystal structure of V30M mutated transthyretin with bromide in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y9c | |||||||||
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Title | Crystal structure of V30M mutated transthyretin with bromide in complex with alpha-mangostin | |||||||||
Components | Transthyretin | |||||||||
Keywords | TRANSPORT PROTEIN/INHIBITOR / transthyretin / natural product / inhibitor / transporter / TRANSPORT PROTEIN-INHIBITOR complex | |||||||||
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: 1.49 Å | |||||||||
Authors | Yokoyama, T. / Mizuguchi, M. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Rep / Year: 2015 Title: Discovery of gamma-Mangostin as an Amyloidogenesis Inhibitor Authors: Yokoyama, T. / Ueda, M. / Ando, Y. / Mizuguchi, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9c.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9c.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 4y9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9c ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9c | HTTPS FTP |
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-Related structure data
Related structure data | 4y9bC 4y9eC 4y9fC 4y9gC 4pweS 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: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M-30 / References: UniProt: P02766 #2: Chemical | #3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 20% PEG400, 0.092 M MES, 0.1 M KBr |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.91714 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91714 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 38146 / % possible obs: 98.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.49→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.3 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PWE Resolution: 1.49→28.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.908 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.216 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→28.54 Å
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Refine LS restraints |
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