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- PDB-5n6q: Xenobiotic reductase A (XenA) from Pseudomonas putida in complex ... -

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Basic information

Entry
Database: PDB / ID: 5n6q
TitleXenobiotic reductase A (XenA) from Pseudomonas putida in complex with 2-phenylacrylic acid
ComponentsNADH:flavin oxidoreductase
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / Profen / ene-reductase / 2-phenylacrylic acid
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
2-Phenylacrylic acid / FLAVIN MONONUCLEOTIDE / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaruppiah, V. / Toogood, H.S. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I015779/1 United Kingdom
CitationJournal: Org. Biomol. Chem. / Year: 2017
Title: Structural insights into the ene-reductase synthesis of profens.
Authors: Waller, J. / Toogood, H.S. / Karuppiah, V. / Rattray, N.J.W. / Mansell, D.J. / Leys, D. / Gardiner, J.M. / Fryszkowska, A. / Ahmed, S.T. / Bandichhor, R. / Reddy, G.P. / Scrutton, N.S.
History
DepositionFeb 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,41813
Polymers81,9042
Non-polymers1,51411
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-92 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.391, 84.041, 155.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40952.047 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 (E. coli) / References: UniProt: Q9R9V9

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Non-polymers , 5 types, 544 molecules

#2: Chemical ChemComp-8OZ / 2-Phenylacrylic acid


Mass: 148.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 7.5 and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.2→77.99 Å / Num. obs: 38419 / % possible obs: 98.4 % / Redundancy: 3.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.118 / Net I/σ(I): 5.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3290 / CC1/2: 0.514 / Rpim(I) all: 0.592 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPM

5cpm


Resolution: 2.2→57.391 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 22.6
RfactorNum. reflection% reflection
Rfree0.2254 2000 5.22 %
Rwork0.1658 --
obs0.1689 38344 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→57.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 96 533 6151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095794
X-RAY DIFFRACTIONf_angle_d0.9397905
X-RAY DIFFRACTIONf_dihedral_angle_d10.7853400
X-RAY DIFFRACTIONf_chiral_restr0.054831
X-RAY DIFFRACTIONf_plane_restr0.0071099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25510.32261400.2532542X-RAY DIFFRACTION98
2.2551-2.31610.28341420.24012585X-RAY DIFFRACTION98
2.3161-2.38420.31941400.22182546X-RAY DIFFRACTION98
2.3842-2.46120.30541410.20382571X-RAY DIFFRACTION99
2.4612-2.54920.23741420.19192570X-RAY DIFFRACTION98
2.5492-2.65120.24571390.1852534X-RAY DIFFRACTION97
2.6512-2.77190.25061370.16942482X-RAY DIFFRACTION94
2.7719-2.9180.25151420.16432601X-RAY DIFFRACTION99
2.918-3.10080.21331440.15892599X-RAY DIFFRACTION99
3.1008-3.34020.21131430.14792610X-RAY DIFFRACTION98
3.3402-3.67630.19571450.13142620X-RAY DIFFRACTION99
3.6763-4.20820.18621460.12452661X-RAY DIFFRACTION99
4.2082-5.30120.17341470.13332675X-RAY DIFFRACTION99
5.3012-57.410.21151520.18592748X-RAY DIFFRACTION97

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