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- PDB-3nk0: Complex of 6-hydroxy-L-nicotine oxidase with inhibitor bound at a... -

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Basic information

Entry
Database: PDB / ID: 3nk0
TitleComplex of 6-hydroxy-L-nicotine oxidase with inhibitor bound at active site and turnover product at exit cavity
Components6-hydroxy-L-nicotine oxidase
KeywordsOXIDOREDUCTASE / ENANTHIOMERIC SUBSTRATE-INHIBITOR / FLAVOENZYMES / NICOTINE DEGRADATION
Function / homology
Function and homology information


(S)-6-hydroxynicotine oxidase / (S)-6-hydroxynicotine oxidase activity / nicotine catabolic process / alkaloid metabolic process / nucleotide binding / cytoplasm
Similarity search - Function
: / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...: / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-GP7 / 5-[(2R)-1-methylpyrrolidin-2-yl]pyridin-2-ol / Chem-HNM / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKachalova, G.S. / Bartunik, H.D.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans.
Authors: Kachalova, G.S. / Bourenkov, G.P. / Mengesdorf, T. / Schenk, S. / Maun, H.R. / Burghammer, M. / Riekel, C. / Decker, K. / Bartunik, H.D.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine from Arthrobacter nicotinovorans
Authors: Kachalova, G.S. / Bourenkov, G.P. / Mengesdorf, T. / Schenk, S. / Maun, H.R. / Burghammer, M. / Riekel, C. / Decker, K. / Bartunik, H.D.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 6-hydroxy-L-nicotine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0465
Polymers47,2141
Non-polymers1,8324
Water8,161453
1
X: 6-hydroxy-L-nicotine oxidase
hetero molecules

X: 6-hydroxy-L-nicotine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,09210
Polymers94,4282
Non-polymers3,6648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area32780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.677, 163.677, 163.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

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Protein , 1 types, 1 molecules X

#1: Protein 6-hydroxy-L-nicotine oxidase


Mass: 47214.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter nicotinovorans (bacteria) / Gene: 6-HLNO / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: Q93NH4, (S)-6-hydroxynicotine oxidase

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Non-polymers , 5 types, 457 molecules

#2: Chemical ChemComp-HNK / 5-[(2R)-1-methylpyrrolidin-2-yl]pyridin-2-ol / 6-hydroxy-D-nicotine


Mass: 178.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-GP7 / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate / 1-pentadecanoyl-2-hexadecanoyl-sn-glycero-3-phosphoethanolamine


Mass: 673.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68NO8P
#5: Chemical ChemComp-HNM / 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one


Mass: 194.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 3.87 Å3/Da / Density % sol: 68.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2003 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 41095 / Num. obs: 40984 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 33.98 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2 / Num. unique all: 2023 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3K7M

3k7m


Resolution: 2.15→14.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.902 / SU ML: 0.102 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21043 2054 5 %RANDOM
Rwork0.16422 ---
obs0.16648 38825 99.43 %-
all-39048 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.234 Å2
Refinement stepCycle: LAST / Resolution: 2.15→14.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 123 453 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0213612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.9884932
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3095457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33323.234167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77615558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1681530
X-RAY DIFFRACTIONr_chiral_restr0.1870.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022782
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21784
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.22410
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5311.52253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37723508
X-RAY DIFFRACTIONr_scbond_it3.82531628
X-RAY DIFFRACTIONr_scangle_it5.7854.51412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 166 -
Rwork0.22 2762 -
obs-2762 99.52 %

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