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- PDB-7kho: NicA2 variant N462V in complex with (S)-nicotine -

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Basic information

Entry
Database: PDB / ID: 7kho
TitleNicA2 variant N462V 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 S16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 10, 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: 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: Amine oxidase
B: Amine oxidase
C: Amine oxidase
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,39312
Polymers214,6024
Non-polymers3,7918
Water30617
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5983
Polymers53,6501
Non-polymers9482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5983
Polymers53,6501
Non-polymers9482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5983
Polymers53,6501
Non-polymers9482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5983
Polymers53,6501
Non-polymers9482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.398, 134.565, 168.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Amine oxidase /


Mass: 53650.422 Da / Num. of mol.: 4 / Mutation: N462V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida S16 (bacteria) / Strain: S16 / Gene: PPS_4081 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8G0P2
#2: Chemical
ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE / Nicotine


Mass: 162.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 9
Details: 0.5 M sodium chloride, 0.15 M Bis-Tris propane pH 9.0, 17% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.69→47.29 Å / Num. obs: 51755 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.93 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1114 / Rpim(I) all: 0.04679 / Rrim(I) all: 0.121 / Net I/σ(I): 12
Reflection shellResolution: 2.69→2.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.6662 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 4629 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.2857 / Rrim(I) all: 0.7264 / % possible all: 89.99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260phasing
PHENIX1.14_3260model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TTK

5ttk


Resolution: 2.69→39.6 Å / SU ML: 0.3621 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.1251 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2857 1843 3.59 %
Rwork0.236 49539 -
obs0.2378 51382 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.15 Å2
Refinement stepCycle: LAST / Resolution: 2.69→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13211 0 260 17 13488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003513774
X-RAY DIFFRACTIONf_angle_d0.793718690
X-RAY DIFFRACTIONf_chiral_restr0.08722040
X-RAY DIFFRACTIONf_plane_restr0.00472393
X-RAY DIFFRACTIONf_dihedral_angle_d3.67117928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.760.41531100.3312988X-RAY DIFFRACTION72.55
2.76-2.840.35811170.31973250X-RAY DIFFRACTION79.69
2.84-2.930.39521270.30453477X-RAY DIFFRACTION84.52
2.93-3.040.42241380.30963542X-RAY DIFFRACTION86.43
3.04-3.160.39631330.29533666X-RAY DIFFRACTION89.22
3.16-3.30.30681430.26833797X-RAY DIFFRACTION92.36
3.3-3.480.27691490.24883947X-RAY DIFFRACTION95.28
3.48-3.70.29171490.2514019X-RAY DIFFRACTION97.27
3.7-3.980.28511530.23354046X-RAY DIFFRACTION97.47
3.98-4.380.30111540.21524099X-RAY DIFFRACTION98.54
4.38-5.020.24041550.20574156X-RAY DIFFRACTION99.22
5.02-6.310.27011550.22454191X-RAY DIFFRACTION99.09
6.31-39.60.22681600.19984361X-RAY DIFFRACTION98.95

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