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- PDB-8bpp: crystal structure of N-ethylmaleimide reductase (nemA) from Esche... -

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Basic information

Entry
Database: PDB / ID: 8bpp
Titlecrystal structure of N-ethylmaleimide reductase (nemA) 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
FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.0Feb 28, 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)120,0566
Polymers118,6873
Non-polymers1,3693
Water59433
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0192
Polymers39,5621
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0192
Polymers39,5621
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0192
Polymers39,5621
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.488, 142.069, 87.871
Angle α, β, γ (deg.)90.000, 107.020, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

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

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

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Components

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


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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 175 mM malic acid, 18% PEG 3350

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Data collection

DiffractionMean temperature: 77 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 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

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
3.1-3.276.51.1110.72587439710.471.2091.1112100
3.27-3.476.10.77412281137620.340.8480.7742.799.5
3.47-3.716.60.5331.42314535150.2250.5790.5333.799.7
3.71-46.60.3372.12189633130.1420.3660.3375.499.8
4-4.386.60.2412.91987530290.1020.2620.2416.999.9
4.38-4.96.40.1733.61776027620.0740.1890.1738.699.7
4.9-5.666.50.1534.21573524140.0650.1670.1538.899.7
5.66-6.9370.144.41444020670.0570.1510.149.8100
6.93-9.86.40.1045.11032916040.0450.1140.10412.399.7
9.8-19.8966.40.0786.750397820.0330.0850.07816.388.1

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Processing

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

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
RfactorNum. reflection% reflection
Rfree0.2632 1999 7.35 %
Rwork0.2297 25185 -
obs0.2321 27184 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.79 Å2 / Biso mean: 58.7287 Å2 / Biso min: 24.34 Å2
Refinement stepCycle: final / Resolution: 3.1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8310 0 93 33 8436
Biso mean--46.15 50.67 -
Num. residues----1086
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5131X-RAY DIFFRACTION8.883TORSIONAL
12B5131X-RAY DIFFRACTION8.883TORSIONAL
13C5131X-RAY DIFFRACTION8.883TORSIONAL
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 (%)
3.1-3.180.33911420.348517841926100
3.18-3.260.36591410.320517901931100
3.26-3.360.39481420.309517831925100
3.36-3.470.33331430.29171804194799
3.47-3.590.3221410.28281772191399
3.59-3.730.30121430.260517991942100
3.73-3.90.26411420.23771791193399
3.9-4.10.27931420.228318051947100
4.1-4.360.30871440.215418141958100
4.36-4.690.21461420.20217791921100
4.69-5.160.25561430.20621800194399
5.16-5.890.20381450.198118221967100
5.89-7.350.2321430.194518091952100
7.36-19.90.17111460.171118331979100

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