[English] 日本語
Yorodumi- PDB-8bpp: crystal structure of N-ethylmaleimide reductase (nemA) from Esche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bpp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | crystal structure of N-ethylmaleimide reductase (nemA) from Escherichia coli | |||||||||
Components | N-ethylmaleimide reductase | |||||||||
Keywords | OXIDOREDUCTASE / old yellow enzyme / OYE / E. coli / maleimide | |||||||||
Function / homology | Function and homology information N-ethylmaleimide reductase activity / nitroglycerin metabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / chromate reductase activity / 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Pfister, P. / Tinzl, M. / Erb, T. | |||||||||
Funding support | Germany, European Union, 2items
| |||||||||
Citation | Journal: To Be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bpp.cif.gz | 215.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bpp.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpp ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpp | HTTPS FTP |
---|
-Related structure data
Related structure data | 3p7yS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||
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
|
-Components
#1: Protein | Mass: 39562.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nemA, ydhN, b1650, JW1642 / Production host: Escherichia coli BL21(DE3) (bacteria) 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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.22 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|