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- PDB-8pa1: Crystal structure of alcohol dehydrogenase/ketoreductase variant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pa1 | ||||||
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Title | Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form | ||||||
![]() | Oxidoreductase, short-chain dehydrogenase/reductase family | ||||||
![]() | OXIDOREDUCTASE / alcohol dehydrogenase / ketoreductase / Short chain dehydrogenase | ||||||
Function / homology | Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / nucleotide binding / Oxidoreductase, short-chain dehydrogenase/reductase family![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rozeboom, H.J. / Janssen, D.B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form Authors: Delgado-Arciniega, E. / Bodescu, V. / Rozeboom, H.J. / Janssen, D.B. / Wijma, H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.7 KB | Display | ![]() |
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PDB format | ![]() | 157.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.4 KB | Display | ![]() |
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Full document | ![]() | 493 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pa2C 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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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 28154.467 Da / Num. of mol.: 4 Mutation: V126P, G128P, V137Y, Q138L, A181F, V187L, A190L, Q204M, M245L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 20 % PEG3350, 0.1 M ammonium sulfate, 0.1 M bis-tris propane pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.8 Å / Num. obs: 31116 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.966 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.101 / Rrim(I) all: 0.182 / Χ2: 0.86 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.6→2.72 Å / % possible obs: 100 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.836 / Num. measured all: 11885 / Num. unique obs: 3805 / CC1/2: 0.449 / Rpim(I) all: 0.563 / Rrim(I) all: 1.012 / Χ2: 1.04 / Net I/σ(I) obs: 1.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.874 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→47.8 Å
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Refine LS restraints |
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