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- PDB-7khn: NicA2 variant N462Y/W427Y in complex with (S)-nicotine -

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Basic information

Entry
Database: PDB / ID: 7khn
TitleNicA2 variant N462Y/W427Y in complex with (S)-nicotine
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / flavoenzyme / oxidoreductase / nicotine / Rossmann-core fold
Function / homology
Function and homology information


nicotine dehydrogenase / nicotine catabolic process / alkaloid metabolic process / periplasmic space / oxidoreductase activity / nucleotide binding
Similarity search - Function
Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / Nicotine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsTararina, M.A. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2021
Title: Fast Kinetics Reveals Rate-Limiting Oxidation and the Role of the Aromatic Cage in the Mechanism of the Nicotine-Degrading Enzyme NicA2.
Authors: Tararina, M.A. / Dam, K.K. / Dhingra, M. / Janda, K.D. / Palfey, B.A. / Allen, K.N.
History
DepositionOct 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8014
Polymers53,6911
Non-polymers1,1103
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.486, 81.486, 166.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

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Components

#1: Protein Amine oxidase


Mass: 53691.426 Da / Num. of mol.: 1 / Mutation: N462Y, W427Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain S16) (bacteria)
Strain: S16 / Gene: PPS_4081 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8G0P2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE


Mass: 162.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.3 M sodium phosphate monobasic monohydrate, 1.0 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.31→81.49 Å / Num. obs: 24936 / % possible obs: 98.03 % / Redundancy: 6 % / Biso Wilson estimate: 47.7 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.04664 / Rrim(I) all: 0.1185 / Net I/σ(I): 15.88
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 2235 / CC1/2: 0.44 / CC star: 0.783 / Rpim(I) all: 0.6767 / % possible all: 90.07

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIX1.14_3260_000phasing
PHENIX1.14_3260_000model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TTK

5ttk


Resolution: 2.31→81.49 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3509 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 1998 8.03 %
Rwork0.1972 22888 -
obs0.201 24886 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.46 Å2
Refinement stepCycle: LAST / Resolution: 2.31→81.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 77 86 3570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473565
X-RAY DIFFRACTIONf_angle_d0.76764837
X-RAY DIFFRACTIONf_chiral_restr0.0786525
X-RAY DIFFRACTIONf_plane_restr0.0051620
X-RAY DIFFRACTIONf_dihedral_angle_d6.35082046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.38971270.3261450X-RAY DIFFRACTION89.76
2.37-2.430.3231310.30221496X-RAY DIFFRACTION91.2
2.43-2.50.39941390.26181588X-RAY DIFFRACTION97.35
2.5-2.580.28971410.25721620X-RAY DIFFRACTION99.77
2.58-2.680.31081440.24631642X-RAY DIFFRACTION99.67
2.68-2.780.34021410.2341619X-RAY DIFFRACTION99.66
2.78-2.910.26971450.23931663X-RAY DIFFRACTION99.5
2.91-3.060.29941410.22341628X-RAY DIFFRACTION99.83
3.06-3.260.27791450.22271667X-RAY DIFFRACTION99.67
3.26-3.510.24521440.19781647X-RAY DIFFRACTION99.56
3.51-3.860.2061460.19071680X-RAY DIFFRACTION99.67
3.86-4.420.21211470.15281671X-RAY DIFFRACTION99.29
4.42-5.570.1871490.15271704X-RAY DIFFRACTION99.2
5.57-81.490.21661580.18211813X-RAY DIFFRACTION98.11

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