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- PDB-8au8: Xenobiotic reductase A from P. putida in complex with ethyl (Z)-2... -

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Basic information

Entry
Database: PDB / ID: 8au8
TitleXenobiotic reductase A from P. putida in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate
ComponentsXenobiotic reductase
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
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: 1.58 Å
AuthorsPolidori, N. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Funddoc.funds-46 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: Xenobiotic reductase
B: Xenobiotic reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,18015
Polymers81,9282
Non-polymers2,25213
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-65 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.165, 157.966, 57.614
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

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Protein , 1 types, 2 molecules AB

#1: Protein Xenobiotic reductase / Xenobiotic reductase A


Mass: 40964.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R9V9

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Non-polymers , 7 types, 766 molecules

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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM halogen mix (30 mM NaF, 30 mM NaBr, 30 mM NaI), 25% MPD, 10% PEG 3350, 100 mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.58→46.55 Å / Num. obs: 196951 / % possible obs: 96.79 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.79 Å2 / CC1/2: 0.965 / Net I/σ(I): 4.05
Reflection shellResolution: 1.58→1.636 Å / Num. unique obs: 19854 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n19

3n19


Resolution: 1.58→45.52 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 20.3068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 1114 1.06 %
Rwork0.1639 103532 -
obs0.1641 104646 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.39 Å2
Refinement stepCycle: LAST / Resolution: 1.58→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 150 753 6477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596097
X-RAY DIFFRACTIONf_angle_d0.91738336
X-RAY DIFFRACTIONf_chiral_restr0.0516864
X-RAY DIFFRACTIONf_plane_restr0.00981109
X-RAY DIFFRACTIONf_dihedral_angle_d12.97432198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.650.30031370.268912746X-RAY DIFFRACTION97.62
1.65-1.740.27321390.216812947X-RAY DIFFRACTION99.81
1.74-1.850.21241400.191612962X-RAY DIFFRACTION99.49
1.85-1.990.19651390.167112895X-RAY DIFFRACTION98.73
1.99-2.190.19091360.157912683X-RAY DIFFRACTION96.96
2.19-2.50.18611360.158212624X-RAY DIFFRACTION95.95
2.5-3.160.17841420.162713183X-RAY DIFFRACTION99.76
3.16-45.520.16451450.143713492X-RAY DIFFRACTION98.58

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