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- PDB-4yil: OYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)AC... -

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Basic information

Entry
Database: PDB / ID: 4yil
TitleOYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)ACRYLATE IN A NON PRODUCTIVE BINDING MODE
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / CATALYTIC ACTIVITY / FMN BINDING
Function / homology
Function and homology information


NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding
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
Chem-4D3 / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 Å
AuthorsSantangelo, S. / Brenna, E. / Stewart, J.D. / Powell III, R.W.
CitationJournal: Adv.Synth.Catal. / Year: 2015
Title: Opposite Enantioselectivity in the Bioreduction of (Z)-beta-Aryl-beta-cyanoacrylates Mediated by the Tryptophan 116 Mutants of Old Yellow Enzyme 1: Synthetic Approach to (R)- and (S)-beta-Aryl-gamma-lactams
Authors: Brenna, E. / Crotti, M. / Gatti, F.G. / Monti, D. / Parmeggiani, F. / Powell III, R.W. / Santangelo, S. / Stewart, J.D.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2765
Polymers44,5671
Non-polymers7094
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-17 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.395, 141.395, 42.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 44566.953 Da / Num. of mol.: 1 / Mutation: W116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET3b / Details (production host): pSA01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02899, NADPH dehydrogenase

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Non-polymers , 5 types, 487 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-4D3 / methyl (2Z)-3-cyano-3-(4-fluorophenyl)prop-2-enoate


Mass: 205.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8FNO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 0.2M MgCl2, 0.1M Na HEPES, 35% PEG 400,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.461→32.52 Å / Num. all: 74409 / Num. obs: 74409 / % possible obs: 98.46 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.29
Reflection shellResolution: 1.461→1.491 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 4.38 / % possible all: 97.19

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOHKLSuite0.95data reduction
SCALEPACKHKLSuite0.95data scaling
PHASER1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBU

4gbu


Resolution: 1.461→32.521 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 1998 2.69 %random selection
Rwork0.1648 72371 --
obs0.1654 74369 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.21 Å2 / Biso mean: 21.8773 Å2 / Biso min: 12.97 Å2
Refinement stepCycle: final / Resolution: 1.461→32.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 56 483 3690
Biso mean--18.24 31.34 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063408
X-RAY DIFFRACTIONf_angle_d1.0874649
X-RAY DIFFRACTIONf_chiral_restr0.08479
X-RAY DIFFRACTIONf_plane_restr0.005613
X-RAY DIFFRACTIONf_dihedral_angle_d13.7721297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.461-1.49760.23841380.21564989512797
1.4976-1.53810.27861400.20095097523798
1.5381-1.58330.21851400.19235093523398
1.5833-1.63440.21791420.18325135527799
1.6344-1.69280.2061410.17775114525599
1.6928-1.76060.22541430.17565152529599
1.7606-1.84070.2421420.17685154529699
1.8407-1.93780.19841440.17225204534899
1.9378-2.05920.18131430.16795190533399
2.0592-2.21810.20141440.164152175361100
2.2181-2.44130.19651450.162752505395100
2.4413-2.79440.17021460.158952875433100
2.7944-3.51990.19611480.16115330547899
3.5199-32.52880.15141420.15275159530192

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