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- PDB-7bn7: Crystal structure of ene-reductase OYE2 from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 7bn7
TitleCrystal structure of ene-reductase OYE2 from S. cerevisiae
ComponentsOYE2 isoform 1
KeywordsOXIDOREDUCTASE / NADPH dehydrogenase
Function / homologyFLAVIN MONONUCLEOTIDE / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRobescu, M.S. / Bergantino, E. / Hall, M. / Cendron, L.
CitationJournal: Acs Catalysis / Year: 2022
Title: Asymmetric Proton Transfer Catalysis by Stereocomplementary Old Yellow Enzymes for C=C Bond Isomerization Reaction
Authors: Robescu, M.S. / Cendron, L. / Bacchin, A. / Wagner, K. / Reiter, T. / Janicki, I. / Merusic, K. / Illek, M. / Aleotti, M. / Bergantino, E. / Hall, M.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OYE2 isoform 1
B: OYE2 isoform 1
C: OYE2 isoform 1
D: OYE2 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,55213
Polymers180,2664
Non-polymers2,2869
Water5,873326
1
A: OYE2 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6153
Polymers45,0671
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OYE2 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7074
Polymers45,0671
Non-polymers6413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: OYE2 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6153
Polymers45,0671
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: OYE2 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6153
Polymers45,0671
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.286, 131.975, 138.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
OYE2 isoform 1 / NADPH dehydrogenase 2 / ene-reductase OYE2


Mass: 45066.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OYE2, GI526_G0002963 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A5PXJ0, NADPH dehydrogenase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8 % w/v PEG 20,000/ 0.1 M Sodium acetate pH 4.5 0.25 M Potassium bromide 8 % v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.45→49.19 Å / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 42.47 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.1 / Num. measured all: 394986
Reflection shellResolution: 2.45→2.538 Å / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 26082 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1oya

1oya


Resolution: 2.45→49.19 Å / SU ML: 0.3143 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 6816 5.05 %
Rwork0.1889 128182 -
obs0.1908 134998 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.49 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12598 0 154 326 13078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011913099
X-RAY DIFFRACTIONf_angle_d1.54217784
X-RAY DIFFRACTIONf_chiral_restr0.08721828
X-RAY DIFFRACTIONf_plane_restr0.00912328
X-RAY DIFFRACTIONf_dihedral_angle_d21.07524827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.30662170.31644268X-RAY DIFFRACTION99.69
2.48-2.510.37622070.31064353X-RAY DIFFRACTION99.63
2.51-2.540.30382330.28544286X-RAY DIFFRACTION99.65
2.54-2.570.29212140.27374325X-RAY DIFFRACTION99.54
2.57-2.60.31622380.28484268X-RAY DIFFRACTION99.65
2.6-2.640.29042390.27054311X-RAY DIFFRACTION99.54
2.64-2.680.32282220.26054189X-RAY DIFFRACTION97.01
2.68-2.720.30032440.24164253X-RAY DIFFRACTION98.97
2.72-2.760.27842500.23294366X-RAY DIFFRACTION99.23
2.76-2.80.28332380.22014178X-RAY DIFFRACTION98.95
2.8-2.850.26652200.21684308X-RAY DIFFRACTION99.15
2.85-2.90.26982160.21894248X-RAY DIFFRACTION99.05
2.9-2.960.27452560.21124238X-RAY DIFFRACTION98.77
2.96-3.020.25082230.21054331X-RAY DIFFRACTION99.02
3.02-3.090.26472150.21344283X-RAY DIFFRACTION99.32
3.09-3.160.26273030.22294210X-RAY DIFFRACTION99.38
3.16-3.240.24282450.21714278X-RAY DIFFRACTION99.3
3.24-3.320.26672630.20574247X-RAY DIFFRACTION99.27
3.32-3.420.22072230.20054281X-RAY DIFFRACTION99.23
3.42-3.530.24591950.18774252X-RAY DIFFRACTION97.14
3.53-3.660.20951900.18874282X-RAY DIFFRACTION98.48
3.66-3.810.19192220.18224244X-RAY DIFFRACTION97.92
3.81-3.980.21811720.1764176X-RAY DIFFRACTION96.11
3.98-4.190.17772160.15434343X-RAY DIFFRACTION99.35
4.19-4.450.20542200.14934320X-RAY DIFFRACTION99.3
4.45-4.790.18712300.14384240X-RAY DIFFRACTION99.03
4.8-5.280.18022450.14814285X-RAY DIFFRACTION98.99
5.28-6.040.19712460.15784235X-RAY DIFFRACTION98.72
6.04-7.60.18062300.16114282X-RAY DIFFRACTION99.3
7.61-49.190.13791840.14434302X-RAY DIFFRACTION98.64

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