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- PDB-8auf: XenA Y183F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-o... -

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Basic information

Entry
Database: PDB / ID: 8auf
TitleXenA Y183F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate
ComponentsNADH:flavin oxidoreductase
KeywordsOXIDOREDUCTASE / Ene-reductase / oxime / FMN / complex
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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-O8I / DI(HYDROXYETHYL)ETHER / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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)83,4108
Polymers81,8722
Non-polymers1,5386
Water17,871992
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-29 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.350, 158.690, 57.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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


Mass: 40936.047 Da / Num. of mol.: 2 / Mutation: Y183F
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-O8I / ethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-pentanoate / ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate


Mass: 173.167 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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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: 1.35→46.5 Å / Num. obs: 316512 / % possible obs: 97.21 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.26 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.38
Reflection shellResolution: 1.351→1.399 Å / Num. unique obs: 15636 / CC1/2: 0.908

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
AutoProcessdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N19

3n19


Resolution: 1.35→46.5 Å / SU ML: 0.0965 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.0344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1598 2100 1.28 %
Rwork0.1479 162134 -
obs0.148 164234 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.25 Å2
Refinement stepCycle: LAST / Resolution: 1.35→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 105 992 6681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056266
X-RAY DIFFRACTIONf_angle_d0.85438586
X-RAY DIFFRACTIONf_chiral_restr0.0767882
X-RAY DIFFRACTIONf_plane_restr0.00651161
X-RAY DIFFRACTIONf_dihedral_angle_d14.85792241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.20971330.190610209X-RAY DIFFRACTION92.47
1.38-1.420.20261350.177310428X-RAY DIFFRACTION94.94
1.42-1.460.18591350.164210467X-RAY DIFFRACTION94.94
1.46-1.50.18161360.154110508X-RAY DIFFRACTION95.36
1.5-1.550.14931370.150610593X-RAY DIFFRACTION96.14
1.55-1.60.15351370.145410571X-RAY DIFFRACTION96.09
1.6-1.670.16631400.147710786X-RAY DIFFRACTION97.72
1.67-1.740.17451410.146510884X-RAY DIFFRACTION98.24
1.74-1.830.15531410.155410879X-RAY DIFFRACTION98.29
1.83-1.950.15691410.15310938X-RAY DIFFRACTION98.97
1.95-2.10.18191430.153411025X-RAY DIFFRACTION99.06
2.1-2.310.16041410.144110923X-RAY DIFFRACTION97.8
2.31-2.640.15141450.150411157X-RAY DIFFRACTION99.56
2.64-3.330.14851450.148411246X-RAY DIFFRACTION99.78
3.33-46.50.15231500.135411520X-RAY DIFFRACTION98.6

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