+Open data
-Basic information
Entry | Database: PDB / ID: 4abu | ||||||
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Title | CRYSTAL STRUCTURE OF TRANSTHYRETIN IN COMPLEX WITH LIGAND C-2 | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT PROTEIN / HORMONE / AMYLOIDOSIS INHIBITION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Tomar, D. / Khan, T. / Singh, R.R. / Mishra, S. / Gupta, S. / Surolia, A. / Salunke, D.M. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites. Authors: Tomar, D. / Khan, T. / Singh, R.R. / Mishra, S. / Gupta, S. / Surolia, A. / Salunke, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4abu.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4abu.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 4abu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4abu_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4abu_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4abu_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4abu_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/4abu ftp://data.pdbj.org/pub/pdb/validation_reports/ab/4abu | HTTPS FTP |
-Related structure data
Related structure data | 4abqC 4abvC 4abwC 4ac2C 4ac4C 4ankC 1dvqS 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: 13421.952 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766 #2: Chemical | #3: 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: 2.4 Å3/Da / Density % sol: 49.1 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: POTASSIUM CHLORIDE, POTASSIUM PHOSPHATE, AMMONIUM SULFATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 16, 2009 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER CMF12 38CU-6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→35.5 Å / Num. obs: 20168 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.86→5.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DVQ Resolution: 1.86→63.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.25 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. FT1 A 1125 AND FT1 B 1125 GENERATE CLOSE CONTACTS WITH COPIES RELATED BY A TWO-FOLD CRYSTALLOGRAPHIC AXIS. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. FT1 A 1125 AND FT1 B 1125 GENERATE CLOSE CONTACTS WITH COPIES RELATED BY A TWO-FOLD CRYSTALLOGRAPHIC AXIS. THEIR OCCUPANCIES HAVE THEREFORE BEEN DEFINED AS 0.5.
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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: 26.923 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→63.87 Å
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