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Yorodumi- PDB-4dew: Crystal Structure of the Wild Type TTR Binding Luteolin (TTRwt:LUT) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dew | ||||||
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Title | Crystal Structure of the Wild Type TTR Binding Luteolin (TTRwt:LUT) | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / beta sandwich / amyloidosis | ||||||
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: 1.899 Å | ||||||
Authors | Trivella, D.B.B. / Polikarpov, I. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Flavonoid interactions with human transthyretin: Combined structural and thermodynamic analysis. Authors: Trivella, D.B. / Dos Reis, C.V. / 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 | 4dew.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dew.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dew_validation.pdf.gz | 1005.6 KB | Display | wwPDB validaton report |
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Full document | 4dew_full_validation.pdf.gz | 1012.9 KB | Display | |
Data in XML | 4dew_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 4dew_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/4dew ftp://data.pdbj.org/pub/pdb/validation_reports/de/4dew | HTTPS FTP |
-Related structure data
Related structure data | 4derC 4desC 4detC 4deuC 3cfmS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
NCS oper: (Code: given Matrix: (-0.993056, 0.117216, 0.010051), Vector: |
-Components
#1: Protein | Mass: 15904.984 Da / Num. of mol.: 2 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: Chemical | #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: 1.88 Å3/Da / Density % sol: 34.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% PEG400, 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 1, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.899→30 Å / Num. all: 19276 / Num. obs: 19276 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.077 / Χ2: 0.944 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CFM Resolution: 1.899→26.007 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.8 Å2 / Biso mean: 28.0992 Å2 / Biso min: 10.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.899→26.007 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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