+Open data
-Basic information
Entry | Database: PDB / ID: 3kgs | ||||||
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Title | V30M mutant human transthyretin (TTR) (apoV30M) pH 7.5 | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / TTR / TRANSTHYRETIN / AMYLOID / Amyloidosis / Hormone / Neuropathy / Polymorphism / Secreted / Thyroid hormone / Transport | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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: 1.8 Å | ||||||
Authors | Trivella, D.B. / Polikarpov, I. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Conformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: implications to tetramer stability and ligand-binding. Authors: Trivella, D.B. / Bleicher, L. / Palmieri, L.C. / Wiggers, H.J. / Montanari, C.A. / Kelly, J.W. / Lima, L.M. / Foguel, D. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kgs.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kgs.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/3kgs ftp://data.pdbj.org/pub/pdb/validation_reports/kg/3kgs | HTTPS FTP |
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-Related structure data
Related structure data | 3kgtC 3kguC 1f41S C: citing same article (ref.) 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: 13809.426 Da / Num. of mol.: 2 / Fragment: UNP residues 20-147 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Production host: Escherichia coli (E. coli) / 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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 26041 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1F41 Resolution: 1.8→22.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.83 / SU B: 2.989 / SU ML: 0.095 / SU R Cruickshank DPI: 0.153 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.146 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.12 Å2 / Biso mean: 20.451 Å2 / Biso min: 7.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→22.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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