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- PDB-8bpq: crystal structure of N-ethylmaleimide reductase with mutation Y18... -

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Basic information

Entry
Database: PDB / ID: 8bpq
Titlecrystal structure of N-ethylmaleimide reductase with mutation Y187F (nemA Y187F) from Escherichia coli
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / old yellow enzyme / OYE / E. coli / maleimide
Function / homology
Function and homology information


N-ethylmaleimide reductase activity / oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / nitroglycerin metabolic process / 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
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Tb-Xo4 / FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPfister, P. / Tinzl, M. / Erb, T.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Max Planck Society190003 Germany
European Research Council (ERC)637675European Union
CitationJournal: 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
DepositionNov 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6779
Polymers118,6393
Non-polymers3,0386
Water12,899716
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5593
Polymers39,5461
Non-polymers1,0132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5593
Polymers39,5461
Non-polymers1,0132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5593
Polymers39,5461
Non-polymers1,0132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.062, 96.062, 100.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein N-ethylmaleimide reductase / NEM reductase / N-ethylmaleimide reducing enzyme


Mass: 39546.289 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 ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 77 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.2110.51.2220.64774745660.3961.2851.2222.4100
2.21-2.359.51.2180.54105643320.4241.2921.2182.799.9
2.35-2.5110.10.9570.74088540640.3171.0090.9574.3100
2.51-2.7110.40.7850.83968538100.2560.8260.7855.4100
2.71-2.9710.50.59513703335180.1910.6260.5957100
2.97-3.32100.4361.33172131760.1440.460.4368.4100
3.32-3.838.90.2952.12536928460.1050.3140.2959.9100
3.83-4.79.50.19732284623970.0670.2080.19711.7100
4.7-6.649.10.1813.31730319070.0620.1920.18111.4100
6.64-24.2718.40.153.6911310820.0530.1590.151298.1

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSBuilt=20200417data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P7Y

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
RfactorNum. reflection% reflection
Rfree0.2446 2001 4.37 %
Rwork0.1932 43796 -
obs0.1955 45797 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.3 Å2 / Biso mean: 26.4277 Å2 / Biso min: 4.27 Å2
Refinement stepCycle: final / Resolution: 2.3→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8307 0 183 716 9206
Biso mean--21.34 23.74 -
Num. residues----1086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.27321400.22232033343100
2.36-2.420.30311380.220131543292100
2.42-2.490.29981440.223531393283100
2.49-2.570.27861360.21631463282100
2.57-2.660.32471510.24853097324898
2.66-2.770.31521460.214231043250100
2.77-2.90.2611420.202731453287100
2.9-3.050.26621410.204530853226100
3.05-3.240.24841400.187931523292100
3.24-3.490.24621450.18313080322599
3.49-3.840.22251500.17383132328299
3.84-4.390.16731300.16213111324199
4.39-5.520.20871400.165331233263100
5.53-24.270.21491580.189831253283100

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