+Open data
-Basic information
Entry | Database: PDB / ID: 2h4e | ||||||
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Title | Crystal structure of Cys10 sulfonated transthyretin | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloid / Sulfite / Transthyretin / Familial amyloidotic polyneuropathy | ||||||
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: 1.45 Å | ||||||
Authors | Gales, L. / Damas, A.M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2007 Title: Structural basis for the protective role of sulfite against transthyretin amyloid formation. Authors: Gales, L. / Saraiva, M.J. / Damas, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h4e.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h4e.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 2h4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/2h4e ftp://data.pdbj.org/pub/pdb/validation_reports/h4/2h4e | HTTPS FTP |
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-Related structure data
Related structure data | 1f86S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13857.425 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | ChemComp-SO4 / | #3: 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: 2.08 Å3/Da / Density % sol: 40.85 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.2M sodium acetate, 2.0 M ammonium sulphate, 6 % glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9786 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→63.4 Å / Num. all: 39635 / Num. obs: 39607 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F86 Resolution: 1.45→63.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.989 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.277 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→63.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.488 Å / Total num. of bins used: 20
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Refinement TLS params. | S11: -0.027 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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