+Open data
-Basic information
Entry | Database: PDB / ID: 7kjj | |||||||||
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Title | Reconstructed ancestor of HIUases and Transthyretins | |||||||||
Components | TTR ancestor | |||||||||
Keywords | TRANSPORT PROTEIN / HORMONE TRANSPORT | |||||||||
Function / homology | 3,5,3',5'-TETRAIODO-L-THYRONINE Function and homology information | |||||||||
Biological species | unidentified (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | |||||||||
Authors | Nagem, R.A.P. / Bleicher, L. / Costa, M.A.F. | |||||||||
Funding support | Brazil, 1items
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Citation | Journal: J.Mol.Evol. / Year: 2021 Title: Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies. Authors: Carrijo de Oliveira, L. / Figueiredo Costa, M.A. / Goncalves Pedersolli, N. / Heleno Batista, F.A. / Migliorini Figueira, A.C. / Salgado Ferreira, R. / Alves Pinto Nagem, R. / Alves Nahum, L. / Bleicher, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kjj.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kjj.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kjj ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kjj | HTTPS FTP |
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-Related 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: 14486.085 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TTR ancestor is a reconstruction of the node right after duplication, corresponding to the ancestor of all modern transthyretins Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Condition 1: 2 M lithium sulfate, 5% (v/v) 2-propanol, 0.1 M magnesium sulfate, 0.2 M sodium acetate pH 4.5 Condition 2: 30% (w/v) PEG 1500, 20% (w/v) PEG 400, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→41.34 Å / Num. obs: 55503 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.037 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7752 / CC1/2: 0.868 / Rrim(I) all: 0.703 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→40.89 Å / SU ML: 0.1069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8035 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→40.89 Å
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Refine LS restraints |
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LS refinement shell |
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