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- PDB-3k7t: Crystal structure of apo-form 6-hydroxy-L-nicotine oxidase, cryst... -

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Basic information

Entry
Database: PDB / ID: 3k7t
TitleCrystal structure of apo-form 6-hydroxy-L-nicotine oxidase, crystal form P3121
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
: / 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 / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.85 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: 6-hydroxy-L-nicotine oxidase
B: 6-hydroxy-L-nicotine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6896
Polymers92,7702
Non-polymers2,9194
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-10 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.957, 122.957, 199.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 46385.219 Da / Num. of mol.: 2
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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C36H68NO8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 4.7 Å3/Da / Density % sol: 73.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 1.5M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: Dec 12, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 41415 / Num. obs: 41084 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 25.3
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Num. unique all: 2038 / Rsym value: 0.75 / % 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: 2.85→16.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.93 / SU ML: 0.345 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32118 2035 5 %RANDOM
Rwork0.27549 ---
obs0.27776 38462 98.14 %-
all-39197 --
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: 72.942 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å21.86 Å20 Å2
2--3.72 Å20 Å2
3----5.58 Å2
Refinement stepCycle: LAST / Resolution: 2.85→16.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 192 42 6774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226890
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.999374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67523.595306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.815151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5151550
X-RAY DIFFRACTIONr_chiral_restr0.1030.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025236
X-RAY DIFFRACTIONr_nbd_refined0.2330.23139
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.23
X-RAY DIFFRACTIONr_mcbond_it1.0211.54286
X-RAY DIFFRACTIONr_mcangle_it1.85326750
X-RAY DIFFRACTIONr_scbond_it2.46732979
X-RAY DIFFRACTIONr_scangle_it4.2564.52624
LS refinement shellResolution: 2.85→2.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 134 -
Rwork0.436 2792 -
obs-2792 99.22 %

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