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Yorodumi- PDB-3p3r: Transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)(2-flu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p3r | ||||||
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Title | Transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)(2-fluorophenyl)methanone | ||||||
Components | Transthyretin | ||||||
Keywords | hormone-binding protein / Hormone / T4 / Retinol Binding Protein | ||||||
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: 1.25 Å | ||||||
Authors | Connelly, S. / Wilson, I.A. | ||||||
Citation | Journal: Sci Transl Med / Year: 2011 Title: Potent kinetic stabilizers that prevent transthyretin-mediated cardiomyocyte proteotoxicity. Authors: Alhamadsheh, M.M. / Connelly, S. / Cho, A. / Reixach, N. / Powers, E.T. / Pan, D.W. / Wilson, I.A. / Kelly, J.W. / Graef, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p3r.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p3r.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 3p3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p3r_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3p3r_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3p3r_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3p3r_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/3p3r ftp://data.pdbj.org/pub/pdb/validation_reports/p3/3p3r | HTTPS FTP |
-Related structure data
Related structure data | 3p3sC 3p3tC 3p3uC 2fbrS 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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Details | Asu contains 2 monomers of the tetramer. 2-fold axis splits the two symmetry related dimers. |
-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicuran Gold / 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: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1. ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 19, 2010 Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing) |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 65516 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.029 / Net I/σ(I): 56.5 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.029 / Num. unique all: 6478 / Rsym value: 0.036 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FBR Resolution: 1.25→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1789 / WRfactor Rwork: 0.1559 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.9072 / SU B: 1.216 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0468 / SU Rfree: 0.0443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 131.1 Å2 / Biso mean: 21.8142 Å2 / Biso min: 8.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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