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- PDB-8vcn: GluER mutant - W66F F269Y Q293T F68Y T36E P263L -

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Basic information

Entry
Database: PDB / ID: 8vcn
TitleGluER mutant - W66F F269Y Q293T F68Y T36E P263L
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / G OXYDANS / OLD YELLOW ENZYME / LACTAM CYCLASE / GLUER MUTANT
Function / homologyOxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / ACETATE ION / FLAVIN MONONUCLEOTIDE / Alkene reductase
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsJeffrey, P.D. / Sorigue, D.R. / Liu, Y. / Hyster, T.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127703-08 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Asymmetric Synthesis of alpha-Chloroamides via Photoenzymatic Hydroalkylation of Olefins.
Authors: Liu, Y. / Bender, S.G. / Sorigue, D. / Diaz, D.J. / Ellington, A.D. / Mann, G. / Allmendinger, S. / Hyster, T.K.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9447
Polymers40,1261
Non-polymers8186
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.887, 90.914, 74.872
Angle α, β, γ (deg.)90.000, 110.131, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-680-

HOH

21A-687-

HOH

31A-809-

HOH

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Components

#1: Protein N-ethylmaleimide reductase / NADH oxidase


Mass: 40126.031 Da / Num. of mol.: 1 / Mutation: T36E, W66F, F68Y, P263L, F269Y, Q293T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: nox, AD934_01855, AD950_09540, EDC20_102158 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E8I9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 4% v/v Tacsimate, pH 4.0, and 20% w/v polyethylene glycol 3350
Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2023
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.47→27.81 Å / Num. obs: 57386 / % possible obs: 98.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 12.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.054 / Rrim(I) all: 0.124 / Χ2: 0.98 / Net I/σ(I): 9
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3661 / CC1/2: 0.711 / Rpim(I) all: 0.368 / Rrim(I) all: 0.831 / Χ2: 0.72 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→27.81 Å / SU ML: 0.1313 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.1978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 2911 5.17 %RANDOM
Rwork0.1573 53420 --
obs0.1587 56331 97.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.08 Å2
Refinement stepCycle: LAST / Resolution: 1.47→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 24 443 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542913
X-RAY DIFFRACTIONf_angle_d0.88633969
X-RAY DIFFRACTIONf_chiral_restr0.081423
X-RAY DIFFRACTIONf_plane_restr0.0062527
X-RAY DIFFRACTIONf_dihedral_angle_d17.63481086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.31811060.26851916X-RAY DIFFRACTION73.74
1.5-1.520.2581250.24812524X-RAY DIFFRACTION94.84
1.52-1.550.24921380.22982482X-RAY DIFFRACTION95.76
1.55-1.580.24141200.2132501X-RAY DIFFRACTION96.18
1.58-1.610.24461370.20562531X-RAY DIFFRACTION96.18
1.61-1.650.25561400.19412519X-RAY DIFFRACTION96.8
1.65-1.690.20981730.18772474X-RAY DIFFRACTION97.24
1.69-1.730.19581340.17822573X-RAY DIFFRACTION97.87
1.73-1.780.21841360.17442596X-RAY DIFFRACTION97.92
1.78-1.830.21231540.16632567X-RAY DIFFRACTION98.73
1.83-1.890.19391560.15732526X-RAY DIFFRACTION98.46
1.89-1.960.16351350.15152618X-RAY DIFFRACTION98.96
1.96-2.030.1671330.15172607X-RAY DIFFRACTION99.28
2.03-2.130.17721260.15242611X-RAY DIFFRACTION99.45
2.13-2.240.16421510.15082588X-RAY DIFFRACTION99.42
2.24-2.380.18121350.15162598X-RAY DIFFRACTION99.42
2.38-2.560.20221300.15442623X-RAY DIFFRACTION99.71
2.56-2.820.16861450.15722643X-RAY DIFFRACTION99.89
2.82-3.230.18041290.14542639X-RAY DIFFRACTION99.96
3.23-4.060.16151530.13062625X-RAY DIFFRACTION99.75
4.06-27.810.15231550.13432659X-RAY DIFFRACTION99.75

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