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Yorodumi- PDB-1e5a: Structure of human transthyretin complexed with bromophenols: a n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e5a | ||||||
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Title | Structure of human transthyretin complexed with bromophenols: a new mode of binding | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | PROTEIN TRANSPORT / TRANSPORT(THYROXINE) / ENVIRONMENTAL POLLUTANTS | ||||||
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: 1.8 Å | ||||||
Authors | Ghosh, M. / Meerts, I.A.T.M. / Cook, A. / Bergman, A. / Brouwer, A. / Johnson, L.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of Human Transthyretin Complexed with Bromophenols : A New Mode of Binding Authors: Ghosh, M. / Meerts, I.A.T.M. / Cook, A. / Bergman, A. / Brouwer, A. / Johnson, L.N. #1: Journal: J.Mol.Biol. / Year: 1978 Title: Structure of Prealbumin: Secondary,Tertiary and Quaternary Interactions Determined by Fourier Refinment at 1.8A. Authors: Blake, C.C.F. / Geisow, M.J. / Oatley, S.J. / Rerat, C. / Rerat, B. #2: Journal: Nature / Year: 1977 Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin : A Model of the Thyroid Hormone Nuclear Receptor ? Authors: Blake, C.C.F. / Oatley, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e5a.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e5a.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e5a_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 1e5a_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 1e5a_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1e5a_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/1e5a ftp://data.pdbj.org/pub/pdb/validation_reports/e5/1e5a | HTTPS FTP |
-Related structure data
Related structure data | 1e3fC 1e4hC 1ttaS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9913, -0.1309, 0.0143), Vector: Details | THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BEGENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC TWO-FOLD AXIS PARALLEL TO Z THROUGH THE ORIGIN OF THIS COORDINATE SYSTEM. | |
-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: PLASMA / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | FUNCTION: THYROID HORMONE-BINDING PROTEIN. PROBABLY TRANSPORTS THYROXINE FROM THE BLOODSTREAM TO ...FUNCTION: THYROID HORMONE-BINDING PROTEIN. PROBABLY TRANSPORTS | |
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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: 2.17 Å3/Da / Density % sol: 43.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 20818 / % possible obs: 92.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.345 / % possible all: 92.8 |
Reflection | *PLUS Num. measured all: 249678 |
Reflection shell | *PLUS % possible obs: 92.8 % / Num. unique obs: 2543 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TTA Resolution: 1.8→20 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE TRIBROMOPHENOL MOLECULE IS LOCATED NEAR THE THYROXINE BINDING SITE BUT NOT SYMMETRICALLY ON THE CRYSTALLOGRAPHIC Z AXIS AS IS THE CASE FOR A SIMILAR COMPOUND PENTABROMOPHENOL. THERE ARE ...Details: THE TRIBROMOPHENOL MOLECULE IS LOCATED NEAR THE THYROXINE BINDING SITE BUT NOT SYMMETRICALLY ON THE CRYSTALLOGRAPHIC Z AXIS AS IS THE CASE FOR A SIMILAR COMPOUND PENTABROMOPHENOL. THERE ARE TWO SYMMETRY EQUIVALENT POSITIONS ABOUT THE TWO FOLD AXIS, EACH WITH AN OCCUPANCY .5 AT EACH OF THE BINDING SITES. WATER MOLECULES W91, W306, W336 LOCATED ON THE SAME SYMMETRY AXIS WERE KEPT FIXED IN POSITION DURING THE REFINEMENT. RESIDUES 1-9 AND 126-127 OF BOTH THE CHAINS WERE NOT OBSERVED IN THE ELECTRON DENSITY MAP.
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Displacement parameters | Biso mean: 18.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.94 Å / Total num. of bins used: 5
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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