+Open data
-Basic information
Entry | Database: PDB / ID: 3a4f | ||||||
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Title | Crystal Structure of Human Transthyretin (E54K) | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / BETA BARREL / Amyloid / Amyloidosis / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Neuropathy / 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: 1.99 Å | ||||||
Authors | Miyata, M. / Sato, T. / Nakamura, T. / Ikemizu, S. / Yamagata, Y. / Kai, H. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Role of the glutamic acid 54 residue in transthyretin stability and thyroxine binding Authors: Miyata, M. / Sato, T. / Mizuguchi, M. / Nakamura, T. / Ikemizu, S. / Nabeshima, Y. / Susuki, S. / Suwa, Y. / Morioka, H. / Ando, Y. / Suico, M.A. / Shuto, T. / Koga, T. / 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 | 3a4f.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4f.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4f ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4f | HTTPS FTP |
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-Related structure data
Related structure data | 3a4dC 3a4eC 1bmzS C: citing same article (ref.) 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: 13777.427 Da / Num. of mol.: 2 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: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS BASED REFERENCE 96 IN THE DATABASE TTHY_HUMAN (UNIPROTKB/SWISS-PROT P02766). E54K ...THE SEQUENCE IS BASED REFERENCE 96 IN THE DATABASE TTHY_HUMAN (UNIPROTKB/SWISS-PROT P02766). E54K IS VARIANT OF TTHY_HUMAN. | |
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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: 2.13 Å3/Da / Density % sol: 42.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 200mM citrate, 3M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, 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: Oct 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 16692 / Rmerge(I) obs: 0.064 / Net I/σ(I): 45.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BMZ Resolution: 1.99→35.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.601 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.415 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→35.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.992→2.043 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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