+Open data
-Basic information
Entry | Database: PDB / ID: 7kcn | ||||||
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Title | Reconstructed ancestor of HIUases and Transthyretins | ||||||
Components | HIUase-TTR ancestor | ||||||
Keywords | UNKNOWN FUNCTION / probably a 5-hydroxyisourate hydrolase | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.46 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 | 7kcn.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kcn.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/7kcn ftp://data.pdbj.org/pub/pdb/validation_reports/kc/7kcn | 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: 13668.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: This protein sequence was designed (reconstructed) to represent an HIUase-TTR ancestor before gene duplication Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.44 Å3/Da / Density % sol: 49.51 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20-24% (w/v) PEG 1,500, 20-30% (v/v) glycerol |
-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 PILATUS 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: 1.46→44.05 Å / Num. obs: 45814 / % possible obs: 97.1 % / Redundancy: 11.5 % / Biso Wilson estimate: 18.72 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.46→1.55 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 11794 / CC1/2: 0.933 / Rrim(I) all: 0.353 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.46→30.1 Å / SU ML: 0.1254 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9076 / 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: 25.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→30.1 Å
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Refine LS restraints |
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LS refinement shell |
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