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- PDB-3weu: Crystal structure of the L-Lys epsilon-oxidase from Marinomonas m... -

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Basic information

Entry
Database: PDB / ID: 3weu
TitleCrystal structure of the L-Lys epsilon-oxidase from Marinomonas mediterranea
ComponentsL-lysine 6-oxidase
KeywordsOXIDOREDUCTASE / amino acid oxidase / arm / beta barrel / three beta sheets / amine oxidase / L-Lys binding
Function / homology
Function and homology information


L-lysine 6-oxidase / L-lysine 6-oxidase activity / negative regulation of single-species biofilm formation / quinone binding / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
L-lysine epsilon-oxidase / L-Lysine epsilon oxidase, N-terminal / L-lysine epsilon oxidase, C-terminal / L-Lysine epsilon oxidase N-terminal / L-lysine epsilon oxidase C-terminal domain
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / L-lysine 6-oxidase
Similarity search - Component
Biological speciesMarinomonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsOkazaki, S. / Nakano, S. / Matsui, D. / Akaji, S. / Inagaki, K. / Asano, Y.
CitationJournal: J.Biochem. / Year: 2013
Title: X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea
Authors: Okazaki, S. / Nakano, S. / Matsui, D. / Akaji, S. / Inagaki, K. / Asano, Y.
History
DepositionJul 12, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
A: L-lysine 6-oxidase
B: L-lysine 6-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,89028
Polymers162,0202
Non-polymers1,87026
Water20,3211128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L-lysine 6-oxidase
B: L-lysine 6-oxidase
hetero molecules

A: L-lysine 6-oxidase
B: L-lysine 6-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,78156
Polymers324,0414
Non-polymers3,74052
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area21290 Å2
ΔGint-85 kcal/mol
Surface area94190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.089, 125.746, 70.591
Angle α, β, γ (deg.)90.00, 99.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1273-

HOH

21B-1421-

HOH

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Components

#1: Protein L-lysine 6-oxidase / L-lysine-epsilon-oxidase / Marinocine


Mass: 81010.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (bacteria) / Strain: NBRC 103028 / Gene: lodA / Production host: Marinomonas mediterranea (bacteria) / Strain (production host): NBRC 103028 / References: UniProt: F2JXJ3, L-lysine 6-oxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M ammonium sulfate, 10%(v/v) 1,4-dioxane, 0.1M MES/NaOH, 0.2M NaI, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 20, 2013
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 124499 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.8 / Num. unique all: 21819 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→47.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.329 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17833 1996 1.6 %RANDOM
Rwork0.1428 ---
obs0.14337 121931 98.42 %-
all-124499 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.737 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.93→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10741 0 114 1128 11983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01911400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210152
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.94815524
X-RAY DIFFRACTIONr_angle_other_deg0.961323427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80951417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87925.017582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.776151743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1971556
X-RAY DIFFRACTIONr_chiral_restr0.1480.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02113366
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022720
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.927→1.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 129 -
Rwork0.139 7771 -
obs--85.5 %

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