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- PDB-3ngc: Complex of 6-hydroxy-L-nicotine oxidase with intermediate methylm... -

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Basic information

Entry
Database: PDB / ID: 3ngc
TitleComplex of 6-hydroxy-L-nicotine oxidase with intermediate methylmyosmine product formed during catalytic turnover
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 / Chem-HNH / 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 11, 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 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)49,0285
Polymers47,2141
Non-polymers1,8144
Water8,251458
1
X: 6-hydroxy-L-nicotine oxidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)98,05610
Polymers94,4282
Non-polymers3,6288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1210 Å2
ΔGint-11 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.766, 162.766, 162.766
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) / Strain: gram-positive soil bacterium / 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, 462 molecules

#2: Chemical ChemComp-HNL / 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / 6-hydroxy-L-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-HNH / 5-(1-methyl-4,5-dihydro-1H-pyrrol-2-yl)pyridin-2-ol / 6-hydroxy-N-Methyl-myosmine


Mass: 176.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 293 K / 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
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: 2.25→20 Å / Num. obs: 34405 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 34.45 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→12.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.542 / SU ML: 0.116 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1735 5 %RANDOM
Rwork0.191 ---
obs0.192 32985 98.5 %-
all-33487 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 2.25→12.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 122 458 3852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0213521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2031.9964796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32223.59156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52915531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0581525
X-RAY DIFFRACTIONr_chiral_restr0.1540.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022686
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21774
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.22412
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5371.52195
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27623427
X-RAY DIFFRACTIONr_scbond_it4.09731575
X-RAY DIFFRACTIONr_scangle_it6.0534.51367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 110 -
Rwork0.223 2327 -
obs--97.21 %

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