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- PDB-9fh7: OYE2 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 9fh7
TitleOYE2 from Saccharomyces cerevisiae
ComponentsNADPH dehydrogenase 2
KeywordsFLAVOPROTEIN / Old Yellow Enzyme / Ene-reductase
Function / homology
Function and homology information


NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding / apoptotic process / mitochondrion / nucleus / cytoplasm
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 / NADPH dehydrogenase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.529 Å
AuthorsOpperman, D.J. / Paul, C.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2024
Title: Asymmetric Monoreduction of alpha , beta-Dicarbonyls to alpha-Hydroxy Carbonyls by Ene Reductases.
Authors: Wolder, A.E. / Heckmann, C.M. / Hagedoorn, P.L. / Opperman, D.J. / Paul, C.E.
History
DepositionMay 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 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: NADPH dehydrogenase 2
B: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2306
Polymers90,1332
Non-polymers1,0974
Water7,800433
1
A: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7074
Polymers45,0671
Non-polymers6413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5232
Polymers45,0671
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.745, 101.265, 160.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-503-

GOL

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Components

#1: Protein NADPH dehydrogenase 2 / Old yellow enzyme 2


Mass: 45066.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OYE2, YHR179W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03558, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium citrate, pH 5, 16% (v/v) PEG 10 000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.529→47.228 Å / Num. obs: 122425 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.063 / Rrim(I) all: 0.136 / Net I/σ(I): 9.9
Reflection shellResolution: 1.529→1.555 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6095 / CC1/2: 0.35 / Rpim(I) all: 0.673 / Rrim(I) all: 1.429 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.2data scaling
autoPROC1.0.5data processing
XDS20180808data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.529→47.228 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.656 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20249 6069 5 %RANDOM
Rwork0.17672 ---
obs0.17799 116355 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.989 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.529→47.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6247 0 74 433 6754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136493
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175867
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6498817
X-RAY DIFFRACTIONr_angle_other_deg1.5221.57613623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35322.391368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.031544
X-RAY DIFFRACTIONr_chiral_restr0.0920.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021410
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4641.5663140
X-RAY DIFFRACTIONr_mcbond_other1.4561.5653139
X-RAY DIFFRACTIONr_mcangle_it2.1442.3463922
X-RAY DIFFRACTIONr_mcangle_other2.1442.3473923
X-RAY DIFFRACTIONr_scbond_it2.6851.8993352
X-RAY DIFFRACTIONr_scbond_other2.6861.93349
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1692.7134895
X-RAY DIFFRACTIONr_long_range_B_refined4.92918.8917478
X-RAY DIFFRACTIONr_long_range_B_other4.87918.6987417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.529→1.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 409 -
Rwork0.29 8552 -
obs--99.97 %

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