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- PDB-8bpq: crystal structure of N-ethylmaleimide reductase with mutation Y18... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bpq | |||||||||
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Title | crystal structure of N-ethylmaleimide reductase with mutation Y187F (nemA Y187F) from Escherichia coli | |||||||||
![]() | N-ethylmaleimide reductase | |||||||||
![]() | OXIDOREDUCTASE / old yellow enzyme / OYE / E. coli / maleimide | |||||||||
Function / homology | ![]() N-ethylmaleimide reductase activity / nitroglycerin metabolic process / chromate reductase activity / oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / xenobiotic metabolic process / FMN binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pfister, P. / Tinzl, M. / Erb, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Development of the Biocatalytic Reductive Aldol Reaction Authors: Tinzl, M. / Stoffel, G.M.M. / Saez, D.A. / Gerlinger, P.D. / Recabarren, R. / Bradley, T. / Westedt, H. / Pfister, P. / Gomez, A. / Ebert, M.O. / Voehringer-Martinez, E. / Erb, T.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 | ![]() | 237.5 KB | Display | ![]() |
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PDB format | ![]() | 188.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bppC ![]() 3p7yS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39546.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P77258, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: Chemical | #4: 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: 2.25 Å3/Da / Density % sol: 45.41 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.2 M Potassium bromide, 0.2 M Potassium thiocyanate, 0.1 M Tris pH 7.8, 3 % w/v PGA (Na+ form, LM) 2 % w/v PEG 3350 5 mM Tb-XO4 |
-Data collection
Diffraction | Mean temperature: 77 K / Ambient temp details: cryostream / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→24.271 Å / Num. obs: 45797 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 17.42 Å2 / Rpim(I) all: 0.148 / Rrim(I) all: 0.467 / Rsym value: 0.442 / Net I/av σ(I): 1.3 / Net I/σ(I): 6.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P7Y Resolution: 2.3→24.27 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.03 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.3 Å2 / Biso mean: 26.4277 Å2 / Biso min: 4.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→24.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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