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- PDB-3k7q: Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase... -

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Basic information

Entry
Database: PDB / ID: 3k7q
TitleCrystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans
Components6-hydroxy-L-nicotine oxidase
KeywordsOXIDOREDUCTASE / ENANTIOMERIC SUBSTRATES / FLAVOENZYMES / NICOTINE DEGRADATION / OXIDASE
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
Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / 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-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.05 Å
AuthorsBourenkov, G.P. / Kachalova, G.S. / Bartunik, H.D.
CitationJournal: 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.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,8524
Polymers47,2141
Non-polymers1,6383
Water6,702372
1
X: 6-hydroxy-L-nicotine oxidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)97,7048
Polymers94,4282
Non-polymers3,2756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1190 Å2
ΔGint-12 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.988, 162.988, 162.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#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
#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 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.89 Å3/Da / Density % sol: 68.37 %
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: ESRF / Beamline: ID13 / Wavelength: 0.782 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 18, 2001 / Details: KB-mirror
RadiationMonochromator: N2 cooled Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 47039 / Num. obs: 47039 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 31.38 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 22
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3282 / Rsym value: 0.71 / % possible all: 100

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Processing

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

3k7m


Resolution: 2.05→12.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.397 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24967 2343 5 %RANDOM
Rwork0.20159 ---
obs0.20398 44208 99.83 %-
all-44283 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 31.389 Å2
Refinement stepCycle: LAST / Resolution: 2.05→12.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 109 372 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0213520
X-RAY DIFFRACTIONr_angle_refined_deg3.0071.9914799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2823.648159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7315532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1921525
X-RAY DIFFRACTIONr_chiral_restr0.2010.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022693
X-RAY DIFFRACTIONr_nbd_refined0.2790.21833
X-RAY DIFFRACTIONr_nbtor_refined0.3510.22451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2366
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.222
X-RAY DIFFRACTIONr_mcbond_it1.8081.52191
X-RAY DIFFRACTIONr_mcangle_it2.7523434
X-RAY DIFFRACTIONr_scbond_it4.29231574
X-RAY DIFFRACTIONr_scangle_it6.4254.51361
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 176 -
Rwork0.209 3150 -
obs-3150 100 %

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