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Yorodumi- PDB-1qwh: a covalent dimer of transthyretin that affects the amyloid pathway -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qwh | ||||||
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Title | a covalent dimer of transthyretin that affects the amyloid pathway | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE/GROWTH FACTOR / thyroid hormone / liver / plasma / cerebrospinal fluid / polyneuropathy / disease mutation / transport / thyroxine / binding protein / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Foss, T. / Kelker, M.S. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Kinetic stabilization of the native state by protein engineering: implications for inhibition of transthyretin amyloidogenesis. Authors: Foss, T.R. / Kelker, M.S. / Wiseman, R.L. / Wilson, I.A. / Kelly, J.W. | ||||||
History |
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Remark 999 | SEQUENCE THIS CONSTRUCT OF TRANSTHYRETIN WAS MADE BY JOINING TWO MONOMERS VIA A GLYCINE RICH ...SEQUENCE THIS CONSTRUCT OF TRANSTHYRETIN WAS MADE BY JOINING TWO MONOMERS VIA A GLYCINE RICH PEPTIDE TO ESSENTIALLY FORM A DIMER OF DIMERS, WHEN IN THE ACTIVE STATE. THE ACTIVE FORM OF THIS CONSTRUCT CRYSTALLIZED WITH HALF OF EACH FULL LENGTH DIMER IN THE ASYMMETRIC UNIT AND WAS ISOMORPHOUS WITH THE STRUCTURE OF 1BZD.PDB. NO ELECTRON DENSITY WAS OBSERVED FOR THE LINKER AND AS SUCH WAS REFINED AS TWO SEPERATE CHAINS (MONOMERS) IN THE ASYMMETRIC UNIT, AS FOR WILD TYPE TRANSTHYRETIN. THE SEQUENCE OF THE LINKER IS GSGGGTGGGSG. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qwh.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qwh.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qwh_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 1qwh_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 1qwh_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1qwh_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/1qwh ftp://data.pdbj.org/pub/pdb/validation_reports/qw/1qwh | HTTPS FTP |
-Related structure data
Related structure data | 1dvqS 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: 12858.368 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A linker, not seen in the density, was used to link chain A and B, see remark 999. Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET29b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 4000, 0.2 M Magnesium Nitrate , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2003 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (ho rizontal focusing) |
Radiation | Monochromator: single crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→30 Å / Num. all: 48411 / Num. obs: 48411 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.053 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.36→29.88 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.539 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DVQ.pdb Resolution: 1.36→29.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.914 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.855 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Total num. of bins used: 20 /
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