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- PDB-7oxl: Crystal structure of human Spermine Oxidase -

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Basic information

Entry
Database: PDB / ID: 7oxl
TitleCrystal structure of human Spermine Oxidase
ComponentsSpermine oxidase,Spermine oxidase,Spermine oxidase
KeywordsUNKNOWN FUNCTION / Spermine oxidase / polyamine metabolism / Spermine / Spermidine
Function / homology
Function and homology information


spermine oxidase / norspermine:oxygen oxidoreductase activity / N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity / PAOs oxidise polyamines to amines / Interconversion of polyamines / spermine:oxygen oxidoreductase (spermidine-forming) activity / polyamine oxidase activity / spermine catabolic process / polyamine biosynthetic process / polyamine catabolic process ...spermine oxidase / norspermine:oxygen oxidoreductase activity / N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity / PAOs oxidise polyamines to amines / Interconversion of polyamines / spermine:oxygen oxidoreductase (spermidine-forming) activity / polyamine oxidase activity / spermine catabolic process / polyamine biosynthetic process / polyamine catabolic process / xenobiotic metabolic process / nuclear membrane / oxidoreductase activity / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FAD-MDL72527 adduct / Spermine oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsImpagliazzo, A. / Johannsson, S. / Thomsen, M. / Krapp, S.
CitationJournal: Commun Biol / Year: 2022
Title: Structure of human spermine oxidase in complex with a highly selective allosteric inhibitor.
Authors: Diaz, E. / Adhikary, S. / Tepper, A.W.J.W. / Riley, D. / Ortiz-Meoz, R. / Krosky, D. / Buyck, C. / Lamenca, C.M. / Llaveria, J. / Fang, L. / Kalin, J.H. / Klaren, V.N.A. / Fahmy, S. / ...Authors: Diaz, E. / Adhikary, S. / Tepper, A.W.J.W. / Riley, D. / Ortiz-Meoz, R. / Krosky, D. / Buyck, C. / Lamenca, C.M. / Llaveria, J. / Fang, L. / Kalin, J.H. / Klaren, V.N.A. / Fahmy, S. / Shaffer, P.L. / Kirkpatrick, R. / Carbajo, R.J. / Thomsen, M. / Impagliazzo, A.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermine oxidase,Spermine oxidase,Spermine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0195
Polymers54,8521
Non-polymers1,1674
Water1,00956
1
A: Spermine oxidase,Spermine oxidase,Spermine oxidase
hetero molecules

A: Spermine oxidase,Spermine oxidase,Spermine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,03710
Polymers109,7032
Non-polymers2,3348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_558-x,-x+y,-z+31
Buried area2410 Å2
ΔGint-66 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.919, 190.919, 43.574
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Spermine oxidase,Spermine oxidase,Spermine oxidase / Polyamine oxidase 1 / PAO-1 / PAOh1


Mass: 54851.699 Da / Num. of mol.: 1 / Fragment: FRAGMENT,FRAGMENT,FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMOX, C20orf16, SMO, UNQ3039/PRO9854 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWM0, spermine oxidase
#2: Chemical ChemComp-6YU / FAD-MDL72527 adduct


Mass: 977.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H53N11O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 29.9999 %v/v MPD, 0.05 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.395→165.34 Å / Num. obs: 28433 / % possible obs: 79.1 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 9
Reflection shellResolution: 2.395→2.436 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.018 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 27492 / % possible all: 16.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: None

Resolution: 2.4→165.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.947 / SU B: 17.159 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 941 3.3 %RANDOM
Rwork0.1854 ---
obs0.1864 27492 79.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.53 Å2 / Biso min: 38.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.37 Å20 Å2
2---0.75 Å2-0 Å2
3---2.42 Å2
Refinement stepCycle: final / Resolution: 2.4→165.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 69 56 3594
Biso mean--58.66 62.93 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133554
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173295
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6684839
X-RAY DIFFRACTIONr_angle_other_deg1.1071.5847555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07321.42176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85315542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7861524
X-RAY DIFFRACTIONr_chiral_restr0.0510.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02823
LS refinement shellResolution: 2.4→2.629 Å / Rfactor Rfree error: 0 /
RfactorNum. reflection
Rfree0.386 6
Rwork0.311 74
Refinement TLS params.Method: refined / Origin x: -26.65 Å / Origin y: 98.072 Å / Origin z: 61.994 Å
111213212223313233
T0.0965 Å2-0.0893 Å20.007 Å2-0.2633 Å20.0458 Å2--0.0425 Å2
L1.1893 °20.0212 °2-0.1129 °2-4.4153 °2-0.2339 °2--1.4843 °2
S0.0344 Å °0.0626 Å °0.1221 Å °-0.0826 Å °0.0037 Å °-0.3083 Å °-0.295 Å °0.0577 Å °-0.0381 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 490
2X-RAY DIFFRACTION1A501

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