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- PDB-8aui: Xenobiotic reductase A Y27F variant in complex with 2-methoxyethy... -

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Basic information

Entry
Database: PDB / ID: 8aui
TitleXenobiotic reductase A Y27F variant in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
ComponentsNADH:flavin oxidoreductase
KeywordsOXIDOREDUCTASE / Ene-reductase / FMN / oxime / TIM-barrel
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-O8R / DI(HYDROXYETHYL)ETHER / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsPolidori, N. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Acs Catalysis / Year: 2023
Title: Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines.
Authors: Breukelaar, W.B. / Polidori, N. / Singh, A. / Daniel, B. / Glueck, S.M. / Gruber, K. / Kroutil, W.
History
DepositionAug 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH:flavin oxidoreductase
B: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,13212
Polymers81,8722
Non-polymers2,26010
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-19 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.770, 84.180, 157.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein NADH:flavin oxidoreductase / Xenobiotic reductase / Xenobiotic reductase A


Mass: 40936.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA, HB4184_21910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R9V9
#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-O8R / 2-methoxyethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-butanoate / 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate


Mass: 189.166 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM (Sodium HEPES; MOPS (acid)) pH 7.5; 30 mM Magnesium chloride hexahydrate; 30 mM Calcium chloride dihydrate; 12,5% v/v MPD; 12,5% PEG 1000; 12,5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.54→45.6 Å / Num. obs: 217359 / % possible obs: 99.41 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.04 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.71
Reflection shellResolution: 1.54→1.595 Å / Num. unique obs: 11124 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n19

3n19


Resolution: 1.54→45.6 Å / SU ML: 0.1438 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1822 1439 1.26 %
Rwork0.1596 112422 -
obs0.1598 113861 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.42 Å2
Refinement stepCycle: LAST / Resolution: 1.54→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 154 809 6535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526073
X-RAY DIFFRACTIONf_angle_d0.80718294
X-RAY DIFFRACTIONf_chiral_restr0.051856
X-RAY DIFFRACTIONf_plane_restr0.00571109
X-RAY DIFFRACTIONf_dihedral_angle_d13.69992174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.60.28211410.28110981X-RAY DIFFRACTION98.09
1.6-1.660.26681420.230611146X-RAY DIFFRACTION99.91
1.66-1.730.22871430.194411165X-RAY DIFFRACTION99.95
1.73-1.830.20971440.177311213X-RAY DIFFRACTION99.85
1.83-1.940.22061420.164411160X-RAY DIFFRACTION99.57
1.94-2.090.19691430.151511151X-RAY DIFFRACTION99.1
2.09-2.30.17431430.147611154X-RAY DIFFRACTION98.78
2.3-2.630.18021450.156511351X-RAY DIFFRACTION99.82
2.63-3.320.18291450.159111377X-RAY DIFFRACTION99.88
3.32-45.60.14491510.13911724X-RAY DIFFRACTION99.21

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