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- PDB-7oy0: Structure of human Spermine Oxidase in complex with a highly sele... -

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Basic information

Entry
Database: PDB / ID: 7oy0
TitleStructure of human Spermine Oxidase in complex with a highly selective allosteric inhibitor
ComponentsSpermine oxidase,Spermine oxidase,Spermine oxidase
KeywordsUNKNOWN FUNCTION / Spermine oxidase / polyamine metabolism / Spermine / Spermidine / inhibitor
Function / homology
Function and homology information


spermine oxidase / PAOs oxidise polyamines to amines / Interconversion of polyamines / spermine oxidase activity / polyamine oxidase activity / polyamine catabolic process / polyamine biosynthetic process / spermine catabolic process / xenobiotic metabolic process / nuclear membrane ...spermine oxidase / PAOs oxidise polyamines to amines / Interconversion of polyamines / spermine oxidase activity / polyamine oxidase activity / polyamine catabolic process / polyamine biosynthetic process / spermine catabolic process / xenobiotic metabolic process / nuclear membrane / 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
Chem-3EI / FAD-MDL72527 adduct / Spermine oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsImpagliazzo, A. / Thomsen, M. / Johannsson, S. / 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 23, 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)56,1734
Polymers54,8521
Non-polymers1,3223
Water1,60389
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)112,3478
Polymers109,7032
Non-polymers2,6436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)193.755, 193.755, 44.332
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
#3: Chemical ChemComp-3EI / 4-[(4-imidazo[1,2-a]pyridin-3-yl-1,3-thiazol-2-yl)amino]phenol


Mass: 308.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N4OS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 4.38 Å3/Da / Density % sol: 71.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.01 M Na Acet, 0.06 M NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.09→167.8 Å / Num. obs: 27031 / % possible obs: 48.2 % / Redundancy: 13 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 18.9
Reflection shellResolution: 2.095→2.4 Å / Redundancy: 15.5 % / Rmerge(I) obs: 1.407 / Mean I/σ(I) obs: 2 / Num. unique obs: 1354 / Rsym value: 1.407 / % possible all: 70

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Processing

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

Resolution: 2.09→167.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.294 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1345 5 %RANDOM
Rwork0.1946 ---
obs0.1968 25687 48.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.04 Å2 / Biso mean: 68.76 Å2 / Biso min: 23.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å2-0 Å2
2---0.42 Å20 Å2
3---1.36 Å2
Refinement stepCycle: final / Resolution: 2.09→167.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 81 89 3791
Biso mean--52.14 51.48 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133754
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173435
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.6735113
X-RAY DIFFRACTIONr_angle_other_deg1.1271.5857898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47721.823192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56215576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7211524
X-RAY DIFFRACTIONr_chiral_restr0.0520.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02868
LS refinement shellResolution: 2.095→2.149 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.265 10 -
obs--24 %
Refinement TLS params.Method: refined / Origin x: 70.706 Å / Origin y: -67.404 Å / Origin z: 19.717 Å
111213212223313233
T0.0571 Å2-0.0621 Å20.0091 Å2-0.3182 Å20.0994 Å2--0.0815 Å2
L0.9021 °20.3934 °2-0.3273 °2-3.1545 °20.2367 °2--1.6775 °2
S0.1011 Å °0.1278 Å °0.1888 Å °0.0463 Å °0.0424 Å °-0.1818 Å °-0.243 Å °-0.0193 Å °-0.1434 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 490
2X-RAY DIFFRACTION1A501

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