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Yorodumi- PDB-1g1o: CRYSTAL STRUCTURE OF THE HIGHLY AMYLOIDOGENIC TRANSTHYRETIN MUTAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g1o | ||||||
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Title | CRYSTAL STRUCTURE OF THE HIGHLY AMYLOIDOGENIC TRANSTHYRETIN MUTANT TTR G53S/E54D/L55S | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT PROTEIN / Greek key / Beta barrel / beta-slip | ||||||
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 / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Eneqvist, T. / Andersson, K. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: The beta-slip: a novel concept in transthyretin amyloidosis. Authors: Eneqvist, T. / Andersson, K. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E. #1: Journal: J.Mol.Biol. / Year: 2000 Title: A Comparative Analysis of 23 Structures of the Amyloidogenic Protein Transthyretin Authors: Hornberg, A. / Eneqvist, T. / Olofsson, A. / Lundgren, E. #2: Journal: Amyloid / Year: 1996 Title: The "edge strand" Hypothesis: Prediction and Test of a Mutational "hot-spot" on the Transthyretin Molecule Associated with FAP Amyloidogenesis Authors: Serpell, L.C. / Goldsteins, G. / Dacklin, I. / Lundgren, E. / Blake, C.C.F. #3: Journal: Biochemistry / Year: 1997 Title: Characterization of Two Highly Amyloidogenic Mutants of Transthyretin Authors: Goldsteins, G. / Andersson, K. / Olofsson, A. / Dacklin, I. / Edvinsson, A. / Baranov, V. / Sandgren, O. / Thylen, C. / Hammarstrom, S. / Lundgren, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g1o.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g1o.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g1o_validation.pdf.gz | 387.4 KB | Display | wwPDB validaton report |
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Full document | 1g1o_full_validation.pdf.gz | 395.8 KB | Display | |
Data in XML | 1g1o_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1g1o_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g1o ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g1o | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13767.280 Da / Num. of mol.: 4 / Mutation: G53S,E54D,L55S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: 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: 2.04 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 5000 MME, sodium citrate, ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.996 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 21080 / Num. obs: 20911 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2960 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. measured all: 109159 |
Reflection shell | *PLUS % possible obs: 98.4 % / Num. unique obs: 2960 / Num. measured obs: 14781 |
-Processing
Software |
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Refinement | Resolution: 2.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 56.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.29 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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