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- PDB-5v4v: Saccharomyces cerevisiae Old Yellow Enzyme 3 -

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Basic information

Entry
Database: PDB / ID: 5v4v
TitleSaccharomyces cerevisiae Old Yellow Enzyme 3
ComponentsNADPH dehydrogenase 3
KeywordsOXIDOREDUCTASE / OYE / flavoprotein / reductase
Function / homology
Function and homology information


NADPH dehydrogenase / pentaerythritol trinitrate reductase activity / NADPH dehydrogenase activity / FMN binding / oxidoreductase activity / apoptotic process
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 / NICOTINAMIDE / NADPH dehydrogenase 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.798 Å
AuthorsStewart, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1111791 United States
CitationJournal: To Be Published
Title: Saccharomyces cerevisiae Old Yellow Enzyme 3
Authors: Stewart, J.D.
History
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH dehydrogenase 3
B: NADPH dehydrogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2828
Polymers89,9412
Non-polymers1,3416
Water16,754930
1
A: NADPH dehydrogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6414
Polymers44,9701
Non-polymers6713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH dehydrogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6414
Polymers44,9701
Non-polymers6713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.214, 107.762, 141.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADPH dehydrogenase 3 / / Old yellow enzyme 3


Mass: 44970.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: OYE3, YPL171C, P2291 / Production host: Escherichia coli (E. coli) / References: UniProt: P41816, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50 mM MES monohydrate, 22% v/v PEG 400, 25 mM Tris, 25 mM NaCl, pH 8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.798→38.88 Å / Num. obs: 87273 / % possible obs: 99.77 % / Redundancy: 14.5 % / Net I/σ(I): 20.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.798→38.879 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.91
RfactorNum. reflection% reflection
Rfree0.1891 4381 5.03 %
Rwork0.1475 --
obs0.1496 87077 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→38.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 92 930 7322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096670
X-RAY DIFFRACTIONf_angle_d1.2459088
X-RAY DIFFRACTIONf_dihedral_angle_d13.932438
X-RAY DIFFRACTIONf_chiral_restr0.052943
X-RAY DIFFRACTIONf_plane_restr0.0061193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7978-1.81820.27271500.25572494X-RAY DIFFRACTION93
1.8182-1.83960.26281460.22582742X-RAY DIFFRACTION100
1.8396-1.86210.27541290.21192747X-RAY DIFFRACTION100
1.8621-1.88560.26131700.21252698X-RAY DIFFRACTION100
1.8856-1.91050.24261340.18932760X-RAY DIFFRACTION100
1.9105-1.93660.23811440.19632731X-RAY DIFFRACTION100
1.9366-1.96430.21321530.192712X-RAY DIFFRACTION99
1.9643-1.99360.23251470.1862724X-RAY DIFFRACTION100
1.9936-2.02480.25241590.18012704X-RAY DIFFRACTION100
2.0248-2.0580.21041340.17792726X-RAY DIFFRACTION100
2.058-2.09340.2161680.17282747X-RAY DIFFRACTION100
2.0934-2.13150.19981510.15492715X-RAY DIFFRACTION100
2.1315-2.17250.18571490.15022750X-RAY DIFFRACTION100
2.1725-2.21680.17851420.14592721X-RAY DIFFRACTION100
2.2168-2.2650.17421510.14062783X-RAY DIFFRACTION100
2.265-2.31770.17911360.13972719X-RAY DIFFRACTION100
2.3177-2.37570.21511420.14262749X-RAY DIFFRACTION100
2.3757-2.43990.19531450.1392777X-RAY DIFFRACTION100
2.4399-2.51170.18381350.13512741X-RAY DIFFRACTION100
2.5117-2.59270.19191520.13742767X-RAY DIFFRACTION100
2.5927-2.68540.18741500.13292756X-RAY DIFFRACTION100
2.6854-2.79290.16411540.12842760X-RAY DIFFRACTION100
2.7929-2.91990.18071220.13062800X-RAY DIFFRACTION100
2.9199-3.07380.17451410.13222800X-RAY DIFFRACTION100
3.0738-3.26630.17961480.13852776X-RAY DIFFRACTION100
3.2663-3.51840.18881260.13532794X-RAY DIFFRACTION100
3.5184-3.87210.16151460.13252842X-RAY DIFFRACTION100
3.8721-4.43180.15241350.11962828X-RAY DIFFRACTION100
4.4318-5.58090.15851610.1262860X-RAY DIFFRACTION100
5.5809-38.88780.17431610.16092973X-RAY DIFFRACTION99

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