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- PDB-8fw1: Gluconobacter Ene-Reductase (GluER) mutant - PagER -

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Basic information

Entry
Database: PDB / ID: 8fw1
TitleGluconobacter Ene-Reductase (GluER) mutant - PagER
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / flavoprotein / 'ene'-reductase / photoenzyme
Function / homologyOxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / NADPH dehydrogenase activity / FMN binding / Aldolase-type TIM barrel / cytosol / FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDahagam, S. / Page, C. / Patterson, M.G. / Hyster, T.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127703-06 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141256 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2023
Title: Regioselective Radical Alkylation of Arenes Using Evolved Photoenzymes.
Authors: Page, C.G. / Cao, J. / Oblinsky, D.G. / MacMillan, S.N. / Dahagam, S. / Lloyd, R.M. / Charnock, S.J. / Scholes, G.D. / Hyster, T.K.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening.
Authors: Lynch, M.L. / Snell, M.E. / Potter, S.A. / Snell, E.H. / Bowman, S.E.J.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)119,9046
Polymers118,5353
Non-polymers1,3693
Water8,431468
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9682
Polymers39,5121
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9682
Polymers39,5121
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9682
Polymers39,5121
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.165, 51.849, 144.935
Angle α, β, γ (deg.)90.510, 90.110, 114.860
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein N-ethylmaleimide reductase / PagER


Mass: 39511.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: nox / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1E8I9
#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.: 468 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 0.1 M potassium bromide, 20% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.5→45.51 Å / Num. obs: 205104 / % possible obs: 96.61 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.077 / Net I/σ(I): 7.9
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.309 / Num. unique obs: 10107 / Rpim(I) all: 0.239 / % possible all: 93.8

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Processing

Software
NameVersionClassification
DIALS3.12.1data reduction
PHENIX1.20.1_4487refinement
PHASER2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MYW

6myw


Resolution: 1.5→45.51 Å / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 25.5365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2728 2021 1 %
Rwork0.2675 201954 -
obs0.2792 203975 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8355 0 93 468 8916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038667
X-RAY DIFFRACTIONf_angle_d0.759811805
X-RAY DIFFRACTIONf_chiral_restr0.07641257
X-RAY DIFFRACTIONf_plane_restr0.00661560
X-RAY DIFFRACTIONf_dihedral_angle_d14.61463171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.42671330.426113475X-RAY DIFFRACTION88.62
1.54-1.580.40051290.400113924X-RAY DIFFRACTION91.61
1.58-1.630.34341540.373214276X-RAY DIFFRACTION94.16
1.63-1.680.31521380.343614346X-RAY DIFFRACTION94.94
1.68-1.740.32431440.316714379X-RAY DIFFRACTION94.79
1.74-1.810.25931200.299914426X-RAY DIFFRACTION95.21
1.81-1.890.25871480.281414499X-RAY DIFFRACTION95.59
1.89-1.990.24721460.258814493X-RAY DIFFRACTION95.46
1.99-2.110.2811510.267914545X-RAY DIFFRACTION96.14
2.11-2.280.27951490.273914631X-RAY DIFFRACTION96.28
2.28-2.510.30241410.27714670X-RAY DIFFRACTION96.79
2.51-2.870.27031520.267614750X-RAY DIFFRACTION97.24
2.87-3.610.25111420.265914702X-RAY DIFFRACTION97.08
3.61-45.510.26951410.241614871X-RAY DIFFRACTION98.13

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