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Open data
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Basic information
Entry | Database: PDB / ID: 7xqm | ||||||
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Title | InDel-mutant short chain Dehydrogenase bound to SAH | ||||||
![]() | Dehydrogenase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Rossmann / mutant / InDel design / coenzyme-switch | ||||||
Function / homology | Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Dehydrogenase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toledo-Patino, S. / Laurino, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insertions and deletions mediated functional divergence of Rossmann fold enzymes. Authors: Toledo-Patino, S. / Pascarelli, S. / Uechi, G.I. / Laurino, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.7 KB | Display | ![]() |
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PDB format | ![]() | 291.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xqnC ![]() 2d1yS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26605.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SAH / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 6% v/v 2-propanol, 0.1 M sodium acetate trihydrate pH 4.5 and 26% v/v polyethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→44.01 Å / Num. obs: 25837 / % possible obs: 98.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.997 / Net I/σ(I): 24.05 |
Reflection shell | Resolution: 2.71→8.13 Å / Num. unique obs: 25801 / CC1/2: 0.996 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2d1y Resolution: 2.71→44.01 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 16.9728 Stereochemistry target values: GeoStd + Monomer Library + 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: 23.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→44.01 Å
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Refine LS restraints |
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LS refinement shell |
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