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Yorodumi- PDB-1gko: An Engineered Transthyretin Monomer that is Non-amyloidogenic - U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gko | ||||||
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Title | An Engineered Transthyretin Monomer that is Non-amyloidogenic - Unless Partially Denatured | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT(THYROXINE) / TRANSTHYRETIN / TTR / MUTANT MONOMER TRANSTHYRETIN / MUTANT MONOMER TTR / AMYLOID FORMING PROTEIN / AMYLOID | ||||||
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: 2.1 Å | ||||||
Authors | Jiang, X. / Smith, C.S. / Petrassi, H.M. / Hammarstrom, P. / White, J.T. / Sacchettini, J.C. / Kelly, J.W. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: An Engineered Transthyretin Monomer that is Nonamyloidogenic, Unless It is Partially Denatured Authors: Jiang, X. / Smith, C.S. / Petrassi, H.M. / Hammarstrom, P. / White, J.T. / Sacchettini, J.C. / Kelly, J.W. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gko.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gko.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gko_validation.pdf.gz | 384.8 KB | Display | wwPDB validaton report |
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Full document | 1gko_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | 1gko_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1gko_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gko ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gko | HTTPS FTP |
-Related structure data
Related structure data | 1bmzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13779.420 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766 #2: Water | ChemComp-HOH / | Compound details | CHAIN A, B, C, D ENGINEERED | |
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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: 2.4 Å3/Da / Density % sol: 41.6 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: microbatch / pH: 8.8 Details: 0.2 M MGCL2, 0.1 M TRIS BUFFER, PH 8.5, 30% W/V POLYETHYLENE GLYCOL 4000 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: other / pH: 8.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: M / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: 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: 1.99→27.17 Å / Num. obs: 27827 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.99→2.06 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 1.5 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BMZ Resolution: 2.1→6 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 / Rfactor Rfree: 0.2755 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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