[English] 日本語
Yorodumi- PDB-1ttc: THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ttc | ||||||
---|---|---|---|---|---|---|---|
Title | THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL30MET VARIANT TO 1.7 ANGSTROMS RESOLUTION | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT(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 / Resolution: 1.7 Å | ||||||
Authors | Hamilton, J.A. / Steinrauf, L.K. / Braden, B.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution. Authors: Hamilton, J.A. / Steinrauf, L.K. / Braden, B.C. / Liepnieks, J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L. #1: Journal: Biochim.Biophys.Acta / Year: 1992 Title: Alteration in Molecular Structure which Results in Disease: The met-30 Variant of Human Plasma Transthyretin Authors: Hamilton, J.A. / Steinrauf, L.K. / Liepnieks, J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ttc.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ttc.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ttc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ttc_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ttc_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 1ttc_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1ttc_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/1ttc ftp://data.pdbj.org/pub/pdb/validation_reports/tt/1ttc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: GLU B 7 - SER B 8 149.677 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO B 102 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98909, 0.14667, 0.01379), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 13809.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Organ: PLASMA / References: UniProt: P02766 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.23 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 5.3 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 25770 / Rmerge(I) obs: 0.063 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.7→5.8 Å / Rfactor obs: 0.179 / σ(F): 2 Details: OCCUPANCIES OF DISORDERED SIDE CHAINS AND ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED ON THE BASIS OF DIFFERENCE FOURIER MAPS. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ...Details: OCCUPANCIES OF DISORDERED SIDE CHAINS AND ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED ON THE BASIS OF DIFFERENCE FOURIER MAPS. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ELECTRON DENSITY. OCCUPANCIES OF SOLVENT MOLECULES WERE REFINED WITH PROLSQ. A NUMBER OF WATER MOLECULE SITES WHICH ARE ONLY PARTIALLY OCCUPIED WERE INCLUDED IN THIS STRUCTURE. BECAUSE OF THIS, SHORT CONTACT DISTANCES ARE FOUND BETWEEN SOME OF THESE WATER MOLECULES. | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5.8 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: 'PROTIN and PROLSQ' / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 19860 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|