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- PDB-2ymw: Structure of the epsilon-lysine oxidase from Marinomonas mediterranea -

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Basic information

Entry
Database: PDB / ID: 2ymw
TitleStructure of the epsilon-lysine oxidase from Marinomonas mediterranea
ComponentsL-LYSINE 6-OXIDASE
KeywordsOXIDOREDUCTASE
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
ETHANOL / L-lysine 6-oxidase
Similarity search - Component
Biological speciesMARINOMONAS MEDITERRANEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.41 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: To be Published
Title: Structure of the Epsilon-Lysine Oxidase from Marinomonas Mediterranea
Authors: Medrano, F.J. / Sanchez-Amat, A. / Romero, A.
History
DepositionOct 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)169,84679
Polymers166,2992
Non-polymers3,54777
Water15,871881
1
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)339,692158
Polymers332,5984
Non-polymers7,094154
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area46290 Å2
ΔGint194.3 kcal/mol
Surface area98440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.680, 127.883, 106.897
Angle α, β, γ (deg.)90.00, 107.18, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein L-LYSINE 6-OXIDASE / L-LYSINE-EPSILON-OXIDASE / MARINOCINE


Mass: 83149.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CYSTEINYL TRYPTOPHYLQUINONE COFACTOR MADE UP BY CYS516 AND TRP581
Source: (gene. exp.) MARINOMONAS MEDITERRANEA (bacteria) / Strain: MMB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: F2JXJ3, L-lysine 6-oxidase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.78 Å3/Da / Density % sol: 55.75 % / Description: NONE
Crystal growpH: 8
Details: 10% ETHANOL, 0.2 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97705
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97705 Å / Relative weight: 1
ReflectionResolution: 2.41→35.28 Å / Num. obs: 68875 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.56 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.2
Reflection shellResolution: 2.41→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.66 / % possible all: 94

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.41→35.28 Å / Cor.coef. Fo:Fc: 0.8754 / Cor.coef. Fo:Fc free: 0.7914 / SU R Cruickshank DPI: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.358 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 3472 5.04 %RANDOM
Rwork0.1919 ---
obs0.1963 68861 98.34 %-
Displacement parametersBiso mean: 42.32 Å2
Baniso -1Baniso -2Baniso -3
1-5.3175 Å20 Å2-6.8357 Å2
2--15.5058 Å20 Å2
3----20.8233 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: LAST / Resolution: 2.41→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10726 0 229 881 11836
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111156HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2115077HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3675SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes338HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1587HARMONIC5
X-RAY DIFFRACTIONt_it11156HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion20.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1398SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12945SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3251 202 4.71 %
Rwork0.2379 4090 -
all0.242 4292 -
obs--98.34 %

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