[English] 日本語
Yorodumi- PDB-3ims: Transthyretin in complex with 2,6-dibromo-4-(2,6-dichlorophenethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ims | ||||||
---|---|---|---|---|---|---|---|
Title | Transthyretin in complex with 2,6-dibromo-4-(2,6-dichlorophenethyl)phenol | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE / Growth Factor / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A | ||||||
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: 1.4 Å | ||||||
Authors | Connelly, S. / Wilson, I.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: A substructure combination strategy to create potent and selective transthyretin kinetic stabilizers that prevent amyloidogenesis and cytotoxicity. Authors: Choi, S. / Reixach, N. / Connelly, S. / Johnson, S.M. / Wilson, I.A. / Kelly, J.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ims.cif.gz | 112.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ims.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ims.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ims_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ims_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ims_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3ims_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/3ims ftp://data.pdbj.org/pub/pdb/validation_reports/im/3ims | HTTPS FTP |
-Related structure data
Related structure data | 3imrC 3imtC 3imuC 3imvC 3imwC 2qgbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.81 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1. ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å |
---|---|
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006 Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing) |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→63.37 Å / Num. obs: 45887 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.04 / Net I/σ(I): 26.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2QGB Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.888 / SU B: 1.857 / SU ML: 0.034 / SU R Cruickshank DPI: 0.068 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 55.58 Å2 / Biso mean: 18.912 Å2 / Biso min: 7.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|