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Yorodumi- PDB-1etb: THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1etb | |||||||||
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Title | THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL 30-->MET 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 | Braden, B.C. / Steinrauf, L.K. / Hamilton, J.A. | |||||||||
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: J.Biol.Chem. / Year: 1993 Title: X-Ray Crystal Structure of the Ala 109(Right Arrow)Thr Variant of Human Transthyretin which Produces Euthyroid Hyperthyroxinemia Authors: Steinrauf, L.K. / Hamilton, J.A. / Braden, B.C. / Murrell, J.R. / Benson, M.D. #2: 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.J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L. | |||||||||
History |
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Remark 700 | SHEET SHEET IDENTIFIERS ARE BASED ON ENTRY 2PAB (PREALBUMIN, BLAKE ET AL.). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1etb.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1etb.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 1etb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1etb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1etb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1etb_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1etb_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/1etb ftp://data.pdbj.org/pub/pdb/validation_reports/et/1etb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: (-0.9904, 0.138, -0.0044), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 2 WHEN APPLIED TO CHAIN 1. | |
-Components
#1: Protein | Mass: 13807.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: PLASMA / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→5 Å / Rfactor obs: 0.163 / σ(F): 2 Details: OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF .001 HAVE NO OBSERVABLE ...Details: OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF .001 HAVE NO OBSERVABLE ELECTRON DENSITY. SOME WATER MOLECULES WERE PLACED IN POSITIONS THAT PROBABLY REPRESENT ALTERNATE CONFORMATIONS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.026 |