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- PDB-5mbx: Crystal structure of reduced murine N1-acetylpolyamine oxidase in... -

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Basic information

Entry
Database: PDB / ID: 5mbx
TitleCrystal structure of reduced murine N1-acetylpolyamine oxidase in complex with N1-acetylspermine
ComponentsPeroxisomal 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 / : / spermine oxidase activity ...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 / : / spermine oxidase 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-SP5 / Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Jan 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7614
Polymers54,6351
Non-polymers1,1263
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-21 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.990, 121.990, 54.910
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 / Polyamine oxidase


Mass: 54634.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE CONTAINS A LOOP DELETION OF RESIDUES 451-458 AND AN INSERION OF A SINGLE GLY RESIDUE AT POSITION 451
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Paox, Pao / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q8C0L6, N1-acetylpolyamine 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-SP5 / N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide / N1-AcSpermine


Mass: 244.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H28N4O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
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. N1-ACETYL SPERMINE WAS ...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. N1-ACETYL SPERMINE WAS SOAKED INTO PRE-FORMED CRYSTAL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.4→40.81 Å / Num. obs: 81328 / % possible obs: 88.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.066 / Net I/σ(I): 20.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4.5 / CC1/2: 0.908 / % possible all: 51.5

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Processing

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

5lae


Resolution: 1.4→40.81 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.2 4187 5.17 %RANDOM
Rwork0.18 ---
obs0.181 80940 88.2 %-
Displacement parametersBiso mean: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.2446 Å20 Å20 Å2
2---0.2446 Å20 Å2
3---0.4892 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.4→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 75 311 4058
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013839HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035220HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1306SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes593HARMONIC5
X-RAY DIFFRACTIONt_it3839HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion15.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion487SEMIHARMONIC5
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_contact4657SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 169 5.6 %
Rwork0.194 2850 -
all0.194 3019 -
obs--44.46 %

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