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Open data
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Basic information
Entry | Database: PDB / ID: 8bj5 | ||||||
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Title | Imine Reductase IR007 from Amycolatopsis azurea | ||||||
![]() | Imine Reductase | ||||||
![]() | OXIDOREDUCTASE / Amine / Imine NADPH / biocatalyst | ||||||
Function / homology | 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NADP binding / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dehydrogenase, putative![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gilio, A.K. / Steflik, J. / Grogan, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Engineering of a Reductive Aminase to Enable the Synthesis of a Key Intermediate to a CDK 2/4/6 Inhibitor Authors: Steflik, J. / Gilio, A. / Burns, M. / Grogan, G. / Kumar, R. / Lewis, R. / Martinez, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.1 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 47.2 KB | Display | |
Data in CIF | ![]() | 64.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bk1C ![]() 6jizS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 30992.225 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAP / #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: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.49 M sodium phosphate; o.91 M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→54.1 Å / Num. obs: 36218 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.12 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.72→2.84 Å / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4351 / CC1/2: 0.95 / Rpim(I) all: 0.38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JIZ Resolution: 2.72→54.1 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.89 / SU B: 17.186 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.189 Å2
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Refinement step | Cycle: 1 / Resolution: 2.72→54.1 Å
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Refine LS restraints |
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