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- PDB-5cpn: Crystal structure of XenA from Pseudomonas putida in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cpn | ||||||
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Title | Crystal structure of XenA from Pseudomonas putida in complex with an NADH mimic (mAc) | ||||||
![]() | Xenobiotic reductase | ||||||
![]() | OXIDOREDUCTASE / XenA / mNADH mimic | ||||||
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. | ||||||
![]() | ![]() 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 | ![]() | 279.4 KB | Display | ![]() |
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PDB format | ![]() | 229.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cplC ![]() 5cpmC ![]() 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.31 % |
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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) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→57.37 Å / Num. obs: 71667 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.1454 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.639 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H90 Resolution: 1.8→57.37 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.31 / 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: 1.8→57.37 Å
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Refine LS restraints |
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LS refinement shell |
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