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- PDB-4ync: OYE1 W116A COMPLEXED WITH (Z)-METHYL-3-CYANO-3-PHENYLACRYLATE IN ... -

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Basic information

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


NADPH dehydrogenase / pentaerythritol trinitrate reductase activity / 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
methyl (2Z)-3-cyano-3-phenylprop-2-enoate / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 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 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2464
Polymers44,5671
Non-polymers6793
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-11 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.503, 141.503, 42.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-857-

HOH

21A-1028-

HOH

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Components

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-4EG / methyl (2Z)-3-cyano-3-phenylprop-2-enoate


Mass: 187.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 0.2M MgCl2, 0.1M NaHEPES, 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: 1.498→27.75 Å / Num. all: 70253 / Num. obs: 70253 / % possible obs: 99.76 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.05
Reflection shellResolution: 1.498→1.551 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 4.65 / % possible all: 99.39

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOHKLSuite 0.95data reduction
SCALEPACKHKLSuite 0.95data scaling
PDB_EXTRACT3.15data extraction
PHENIX1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBU

4gbu


Resolution: 1.498→27.751 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 1998 2.84 %
Rwork0.1554 68241 -
obs0.1559 70239 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.04 Å2 / Biso mean: 18.988 Å2 / Biso min: 9.97 Å2
Refinement stepCycle: final / Resolution: 1.498→27.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 55 545 3751
Biso mean--17.79 29.39 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063406
X-RAY DIFFRACTIONf_angle_d1.1054646
X-RAY DIFFRACTIONf_chiral_restr0.081479
X-RAY DIFFRACTIONf_plane_restr0.005615
X-RAY DIFFRACTIONf_dihedral_angle_d13.9981297
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 (%)
1.4978-1.53520.22871400.18844790493099
1.5352-1.57670.21721410.17648094950100
1.5767-1.62310.19151400.173347884928100
1.6231-1.67550.20211410.162948114952100
1.6755-1.73540.22551420.160648314973100
1.7354-1.80490.19631420.164548254967100
1.8049-1.8870.18261410.158248364977100
1.887-1.98640.16411420.154848554997100
1.9864-2.11090.18371420.157348735015100
2.1109-2.27380.17741440.155648935037100
2.2738-2.50250.17071430.155748835026100
2.5025-2.86420.20431430.155449365079100
2.8642-3.60740.1471470.155549815128100
3.6074-27.75580.14891500.14315130528098

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