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- PDB-3k7m: Crystal structure of 6-hydroxy-L-nicotine oxidase from Arthrobact... -

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Basic information

Entry
Database: PDB / ID: 3k7m
TitleCrystal structure of 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 ...: / 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 / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,6743
Polymers47,2141
Non-polymers1,4592
Water11,079615
1
X: 6-hydroxy-L-nicotine oxidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)97,3476
Polymers94,4282
Non-polymers2,9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1170 Å2
ΔGint-11 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.919, 163.920, 163.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11X-1091-

HOH

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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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.05
SYNCHROTRONMPG/DESY, HAMBURG BW621.05, 0.9185, 0.9207, 0.900
SYNCHROTRONMPG/DESY, HAMBURG BW631.05
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDSep 23, 2000mirrors
MAR CCD 165 mm2CCDSep 24, 2000mirrors
MAR CCD 165 mm3CCDSep 24, 2000mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
3GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.91851
30.92071
40.91
ReflectionResolution: 1.95→20 Å / Num. all: 55137 / Num. obs: 54917 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 15 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 28.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3 / Num. unique all: 3615 / Rsym value: 0.623 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXSphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→14.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.778 / SU ML: 0.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: ISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 2762 5.1 %RANDOM
Rwork0.17607 ---
obs0.17796 51689 99.26 %-
all-52074 --
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: 33.324 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 96 618 4048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0223506
X-RAY DIFFRACTIONr_angle_refined_deg2.631.9894775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24823.613155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59515543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251525
X-RAY DIFFRACTIONr_chiral_restr0.2380.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022664
X-RAY DIFFRACTIONr_nbd_refined0.2290.21741
X-RAY DIFFRACTIONr_nbtor_refined0.3270.22411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2490
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.227
X-RAY DIFFRACTIONr_mcbond_it1.8631.52228
X-RAY DIFFRACTIONr_mcangle_it2.60323442
X-RAY DIFFRACTIONr_scbond_it4.41131560
X-RAY DIFFRACTIONr_scangle_it6.2814.51331
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 190 -
Rwork0.218 3725 -
obs-3725 99.62 %

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