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- PDB-6c71: Nicotine Oxidoreductase in Complex with S-nicotine -

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Basic information

Entry
Database: PDB / ID: 6c71
TitleNicotine Oxidoreductase in Complex with S-nicotine
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Monoamine oxidase family / Nicotine / Substrate specificity
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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
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: 2.649 Å
AuthorsTararina, M.A. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2018
Title: Crystallography Coupled with Kinetic Analysis Provides Mechanistic Underpinnings of a Nicotine-Degrading Enzyme.
Authors: Tararina, M.A. / Xue, S. / Smith, L.C. / Muellers, S.N. / Miranda, P.O. / Janda, K.D. / Allen, K.N.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)218,45312
Polymers214,6624
Non-polymers3,7918
Water1,892105
1
A: Amine oxidase
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2266
Polymers107,3312
Non-polymers1,8964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-8 kcal/mol
Surface area28570 Å2
MethodPISA
2
C: Amine oxidase
hetero molecules

D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2266
Polymers107,3312
Non-polymers1,8964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area7010 Å2
ΔGint-7 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.763, 135.105, 167.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Amine oxidase /


Mass: 53665.395 Da / Num. of mol.: 4
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 (E. coli) / Strain (production host): BL21(DE3) / 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 / 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.: 105 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.3 M sodium chloride, 0.1 M Bis-Tris propane pH 9.0, 15% w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.649→44.98 Å / Num. obs: 57278 / % possible obs: 98.6 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Net I/σ(I): 6.17
Reflection shellResolution: 2.649→2.744 Å / Rmerge(I) obs: 0.717 / Num. unique obs: 5054 / CC1/2: 0.11 / % possible all: 71.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASER1.11.1_2575:000phasing
PHENIX1.11.1_2575:000model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TTK

5ttk


Resolution: 2.649→37.755 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2257 1868 3.47 %
Rwork0.1916 --
obs0.1928 53818 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.649→37.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13637 0 260 105 14002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614222
X-RAY DIFFRACTIONf_angle_d1.05919304
X-RAY DIFFRACTIONf_dihedral_angle_d8.428174
X-RAY DIFFRACTIONf_chiral_restr0.1032098
X-RAY DIFFRACTIONf_plane_restr0.0062479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6489-2.72050.39931020.32282897X-RAY DIFFRACTION68
2.7205-2.80050.36321220.28423554X-RAY DIFFRACTION84
2.8005-2.89090.2891310.25853724X-RAY DIFFRACTION87
2.8909-2.99420.25681370.2443862X-RAY DIFFRACTION91
2.9942-3.1140.281470.23573898X-RAY DIFFRACTION92
3.114-3.25570.25061480.22454065X-RAY DIFFRACTION95
3.2557-3.42720.26471470.21344128X-RAY DIFFRACTION96
3.4272-3.64180.28191500.20514205X-RAY DIFFRACTION98
3.6418-3.92270.22521530.18534213X-RAY DIFFRACTION98
3.9227-4.31690.19661540.16314284X-RAY DIFFRACTION99
4.3169-4.94040.18221570.14814292X-RAY DIFFRACTION99
4.9404-6.21990.18371580.17844352X-RAY DIFFRACTION99
6.2199-37.75840.19071620.16834476X-RAY DIFFRACTION98

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