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Yorodumi- PDB-3ng5: Crystal Structure of V30M transthyretin complexed with (-)-epigal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ng5 | ||||||
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Title | Crystal Structure of V30M transthyretin complexed with (-)-epigallocatechin gallate (EGCG) | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / RETINOL-BINDING / SECRETED / THYROID HORMONE / TRANSPORT / VITAMIN A / THYROXINE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Miyata, M. / Nakamura, T. / Ikemizu, S. / Chirifu, M. / Yamagata, Y. / Kai, H. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal structure of green tea polyphenol(-)-epigallocatechin gallate (EGCG)-transthyretin complex reveals novel binding site distinct from thyroxine binding site Authors: Miyata, M. / Sato, T. / Kugimiya, M. / Sho, M. / Nakamura, T. / Ikemizu, S. / Chirifu, M. / Mizuguchi, M. / Nabeshima, Y. / Suwa, Y. / Morioka, H. / Arimori, T. / Suico, M.A. / Shuto, T. / ...Authors: Miyata, M. / Sato, T. / Kugimiya, M. / Sho, M. / Nakamura, T. / Ikemizu, S. / Chirifu, M. / Mizuguchi, M. / Nabeshima, Y. / Suwa, Y. / Morioka, H. / Arimori, T. / Suico, M.A. / Shuto, T. / Sako, Y. / Momohara, M. / Koga, T. / Morino-Koga, S. / Yamagata, Y. / Kai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ng5.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ng5.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ng5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ng5 ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ng5 | HTTPS FTP |
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-Related structure data
Related structure data | 1bmzS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13809.426 Da / Num. of mol.: 2 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: PET22(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P02766 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.24 Å3/Da / Density % sol: 45.16 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.3 Details: 200MM CITRATE, 3M AMMONIUM SULFATE, pH 5.3, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2008 |
Radiation | Monochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 28169 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 75.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2767 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BMZ Resolution: 1.7→33.657 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.843 / SU ML: 0.26 / σ(F): 1.54 / 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 / Bsol: 62.313 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.53 Å2 / Biso mean: 37.751 Å2 / Biso min: 10.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33.657 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: 10
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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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