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Yorodumi- PDB-1tta: THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tta | ||||||
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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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tta.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tta.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tta_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
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Full document | 1tta_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | 1tta_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1tta_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/1tta ftp://data.pdbj.org/pub/pdb/validation_reports/tt/1tta | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98814, 0.15334, -0.00848), Vector: Details | MONOMERS A AND B OF THE DIMER ARE RELATED TO EACH OTHER BY A PSEUDO TWO-FOLD AXIS APPROXIMATELY PARALLEL TO THE CRYSTALLOGRAPHIC 'B' DIRECTION, PERPENDICULAR TO THE SURFACE OF THE SHEETS, AND PASSING BETWEEN THE H STRAND OF ONE MONOMER AND THE H STRAND OF THE OTHER. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. TWO AB DIMERS ARE ROTATED AROUND THE TWO-FOLD CRYSTALLOGRAPHIC AXIS TO FORM THE TETRAMER, AB-A'B'. | |
-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) / References: UniProt: P02766 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.39 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion / pH: 5.3 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Num. all: 26178 / Rmerge(I) obs: 0.053 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.7→5 Å / σ(F): 2 Details: OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED TO FLATTEN THE FINAL FO-FC ...Details: OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED TO FLATTEN THE FINAL FO-FC DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ELECTRON DENSITY. SHEET IDENTIFIERS ARE BASED ON PROTEIN DATA BANK ENTRY 2PAB (PREALBUMIN, OATLEY AND BLAKE)
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Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
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Refine LS restraints |
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Software | *PLUS Name: prolsq / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 5 Å / Num. reflection obs: 19882 / σ(F): 2 / Rfactor obs: 0.168 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |