+Open data
-Basic information
Entry | Database: PDB / ID: 2g3x | ||||||
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Title | Crystal structure of Transthyretin mutant I84S at acidic pH | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / TTR / amyloid fibrils / point mutation | ||||||
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: 1.58 Å | ||||||
Authors | Pasquato, N. / Folli, C. / Berni, R. / Zanotti, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin. Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G. #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. / Sauer-Eriksson, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g3x.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g3x.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 2g3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g3x_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 2g3x_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 2g3x_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2g3x_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/2g3x ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g3x | HTTPS FTP |
-Related structure data
Related structure data | 2g3zC 2g4eC 2g4gC 2noyC 1f41S S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological unit is a tetramer, obtained by the dimer contained in the asymmetric unit for rotation around the crystallographic two-fold axis (-x,-y,z). |
-Components
#1: Protein | Mass: 13751.280 Da / Num. of mol.: 2 / Mutation: I84S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET11b / 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: 2.03 Å3/Da / Density % sol: 39.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 15% PEG monomethyl ether, 0.1M ammonium sulphate, 50mM sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2005 / Details: Mirrors |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→32.32 Å / Num. all: 30436 / Num. obs: 30436 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.064 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.58→1.68 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.306 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F41 Resolution: 1.58→32.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1594703.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: SHELXL-97 was also used as a refinement program. CNS was used in the final stages of refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.0596 Å2 / ksol: 0.391385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→32.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.68 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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