+Open data
-Basic information
Entry | Database: PDB / ID: 5cpm | ||||||
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Title | XenA from Pseudomonas putida in complex with NADPH4. | ||||||
Components | Xenobiotic reductase | ||||||
Keywords | OXIDOREDUCTASE / XenA | ||||||
Function / homology | Function and homology information NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Knaus, T. / Paul, C.E. / Levy, C.W. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cpm.cif.gz | 315 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cpm.ent.gz | 253.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/5cpm ftp://data.pdbj.org/pub/pdb/validation_reports/cp/5cpm | HTTPS FTP |
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-Related structure data
Related structure data | 5cplC 5cpnC 5cpoC 2h90S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Pseudomonas putida (bacteria) / Gene: xenA / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R9V9 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: NADPH4 complex was grown from 0.06 M (magnesium chloride, calcium chloride), 0.1 M (Tris (base), Bicine) buffer system pH 8.5, 30 % v/v GOL P4K (60% v/v Glycerol: PEG 4K) (Morpheus HT96 A11 Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99 Å |
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: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→74.16 Å / Num. obs: 122500 / % possible obs: 99 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.48 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.251 / Mean I/σ(I) obs: 1.92 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H90 Resolution: 1.5→74.16 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.75 / 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: 1.5→74.16 Å
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Refine LS restraints |
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LS refinement shell |
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