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- PDB-9kuh: Co-crystal structure of wild-type OYE2 with 2-(prop-1-en-2-yl)pyridine -

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Basic information

Entry
Database: PDB / ID: 9kuh
TitleCo-crystal structure of wild-type OYE2 with 2-(prop-1-en-2-yl)pyridine
ComponentsNADPH dehydrogenase 2
KeywordsOXIDOREDUCTASE / Old yellow enzyme 2 / 2-isopropenylpyridine
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 S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsWu, D.S. / Yang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Jacs Au / Year: 2025
Title: Enantioselective Radical Hydrocyanoalkylation of Alkenes via Photoenzymatic Catalysis.
Authors: Wu, D. / Sun, Z. / Wang, S. / Yang, J. / He, J. / Lei, X.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH dehydrogenase 2
B: NADPH dehydrogenase 2
C: NADPH dehydrogenase 2
D: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,2119
Polymers180,2664
Non-polymers1,9455
Water00
1
A: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5232
Polymers45,0671
Non-polymers4561
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6423
Polymers45,0671
Non-polymers5762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADPH dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5232
Polymers45,0671
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.927, 99.198, 119.175
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 45066.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: OYE2, YHR179W / Production host: Escherichia coli (E. coli) / References: UniProt: Q03558, 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-A1EG5 / 2-prop-1-en-2-ylpyridine


Mass: 119.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N / Feature type: SUBJECT OF INVESTIGATION
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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Bicine-tris (pH = 7.5) , 0.2 M sodium potassium tartrate tetrahydrate, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.43→114.61 Å / Num. obs: 29323 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.914 / Rmerge(I) obs: 0.323 / Rpim(I) all: 0.139 / Rrim(I) all: 0.352 / Χ2: 0.71 / Net I/σ(I): 4.7 / Num. measured all: 190908
Reflection shellResolution: 3.43→3.52 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.867 / Num. measured all: 14360 / Num. unique obs: 2152 / CC1/2: 0.7 / Rpim(I) all: 0.365 / Rrim(I) all: 0.943 / Χ2: 0.71 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BN7

7bn7


Resolution: 3.43→23.31 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1437 4.93 %
Rwork0.2016 --
obs0.2047 29156 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.43→23.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12421 0 133 0 12554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.192
X-RAY DIFFRACTIONf_dihedral_angle_d10.1511767
X-RAY DIFFRACTIONf_chiral_restr0.0611820
X-RAY DIFFRACTIONf_plane_restr0.0112306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.43-3.550.34621450.27142738X-RAY DIFFRACTION100
3.55-3.690.29791350.24852762X-RAY DIFFRACTION99
3.69-3.860.27931360.23362751X-RAY DIFFRACTION100
3.86-4.060.2931340.21772756X-RAY DIFFRACTION100
4.06-4.320.24531410.19352780X-RAY DIFFRACTION100
4.32-4.650.23261710.17652725X-RAY DIFFRACTION100
4.65-5.110.22161260.1742787X-RAY DIFFRACTION100
5.11-5.840.24971580.18992778X-RAY DIFFRACTION100
5.84-7.320.29921420.19742802X-RAY DIFFRACTION100
7.32-23.310.21851490.16422840X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 36.9845 Å / Origin y: 17.4079 Å / Origin z: -20.1014 Å
111213212223313233
T0.2528 Å20.0381 Å2-0.0223 Å2-0.2125 Å20.0488 Å2--0.251 Å2
L0.2016 °2-0.0304 °2-0.0556 °2-0.3416 °20.204 °2--0.5107 °2
S0.0358 Å °0.07 Å °0.0322 Å °-0.1324 Å °-0.0385 Å °0.0289 Å °-0.0645 Å °-0.0527 Å °0.0067 Å °
Refinement TLS groupSelection details: all

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