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- PDB-8bpp: crystal structure of N-ethylmaleimide reductase (nemA) from Esche... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bpp | |||||||||
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Title | crystal structure of N-ethylmaleimide reductase (nemA) 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 | ![]() | 215.2 KB | Display | ![]() |
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PDB format | ![]() | 171.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bpqC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 365 / Label seq-ID: 4 - 365
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Components
#1: Protein | Mass: 39562.289 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: 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: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 175 mM malic acid, 18% PEG 3350 |
-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 EIGER2 X 16M / Detector: PIXEL / Date: Oct 21, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→19.9 Å / Num. obs: 27219 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.58 Å2 / Rpim(I) all: 0.109 / Rrim(I) all: 0.278 / Rsym value: 0.255 / Net I/av σ(I): 2.6 / Net I/σ(I): 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P7Y Resolution: 3.1→19.9 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.38 / 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: 125.79 Å2 / Biso mean: 58.7287 Å2 / Biso min: 24.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→19.9 Å
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Refine LS restraints NCS |
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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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