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- PDB-5cpl: The crystal structure of Xenobiotic reductase A (XenA) from Pseud... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cpl | |||||||||
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Title | The crystal structure of Xenobiotic reductase A (XenA) from Pseudomonas putida in complex with a nicotinamide mimic (mNH2) | |||||||||
![]() | Xenobiotic reductase | |||||||||
![]() | OXIDOREDUCTASE / Reductase / Nicotinamide mimic / biomimetic | |||||||||
Function / homology | ![]() NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Knaus, T. / Paul, C.E. / Levy, C.W. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes. Authors: Knaus, T. / Paul, C.E. / Levy, C.W. / de Vries, S. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290.5 KB | Display | ![]() |
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PDB format | ![]() | 236.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cpmC ![]() 5cpnC ![]() 5cpoC ![]() 2h90S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 40964.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate buffer pH 6.5, 40% v/v PEG 300 (JCSG+ HT96 A10 Molecular Dimensions) Temp details: Incubator |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→47.02 Å / Num. all: 102314 / Num. obs: 102314 / % possible obs: 98 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.0679 / Net I/σ(I): 17.41 |
Reflection shell | Resolution: 1.57→1.626 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.91 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H90 Resolution: 1.57→47.02 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 14.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→47.02 Å
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Refine LS restraints |
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LS refinement shell |
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