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- PDB-5lgb: Crystal structure of murine N1-acetylpolyamine oxidase in complex... -

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Basic information

Entry
Database: PDB / ID: 5lgb
TitleCrystal structure of murine N1-acetylpolyamine oxidase in complex with MDL72527
ComponentsPeroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
KeywordsOXIDOREDUCTASE / flavin amine oxidase
Function / homology
Function and homology information


N1-acetylpolyamine oxidase / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity / putrescine catabolic process / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process ...N1-acetylpolyamine oxidase / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity / putrescine catabolic process / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process / spermidine catabolic process / Peroxisomal protein import / peroxisomal matrix
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FAD-MDL72527 adduct / N,N'-BIS(2,3-BUTADIENYL)-1,4-BUTANE-DIAMINE / Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSjogren, T. / Aagaard, A. / Wassvik, C. / Snijder, A. / Barlind, L.
CitationJournal: Biochemistry / Year: 2017
Title: The Structure of Murine N(1)-Acetylspermine Oxidase Reveals Molecular Details of Vertebrate Polyamine Catabolism.
Authors: Sjogren, T. / Wassvik, C.M. / Snijder, A. / Aagaard, A. / Kumanomidou, T. / Barlind, L. / Kaminski, T.P. / Kashima, A. / Yokota, T. / Fjellstrom, O.
History
DepositionJul 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8053
Polymers54,6351
Non-polymers1,1702
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint5 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.080, 121.080, 55.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase / Polyamine oxidase


Mass: 54634.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Paox, Pao / Plasmid: PET24A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C0L6, N1-acetylpolyamine oxidase
#2: Chemical ChemComp-6YU / FAD-MDL72527 adduct


Mass: 977.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H53N11O15P2
#3: Chemical ChemComp-MD2 / N,N'-BIS(2,3-BUTADIENYL)-1,4-BUTANE-DIAMINE / MDL72527


Mass: 192.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: PROTEIN AT 23MG/ML IN 20 MM HEPES, PH 7.0, 100 MM NACL, 5% (V/V) GLYCEROL AND 2.5 MM TCEP WAS EQUILIBRATED AGAINST 2.2 M (NH4)2SO4, 0.2 M NASCN, 0.1 M TRIS PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→40.72 Å / Num. obs: 42850 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 32.56 Å2 / Net I/σ(I): 23.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LAE

5lae


Resolution: 1.8→40.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2157 5.03 %RANDOM
Rwork0.176 ---
obs0.177 42850 100 %-
Displacement parametersBiso mean: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.487 Å20 Å20 Å2
2---1.487 Å20 Å2
3---2.9739 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.8→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 81 166 3786
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013706HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15024HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1255SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes568HARMONIC5
X-RAY DIFFRACTIONt_it3706HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion16.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion470SEMIHARMONIC5
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_contact4275SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 153 4.86 %
Rwork0.194 2998 -
all0.196 3151 -
obs--99.97 %

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