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Yorodumi- PDB-7oy0: Structure of human Spermine Oxidase in complex with a highly sele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oy0 | ||||||
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Title | Structure of human Spermine Oxidase in complex with a highly selective allosteric inhibitor | ||||||
Components | Spermine oxidase,Spermine oxidase,Spermine oxidase | ||||||
Keywords | UNKNOWN FUNCTION / Spermine oxidase / polyamine metabolism / Spermine / Spermidine / inhibitor | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Impagliazzo, A. / Thomsen, M. / Johannsson, S. / Krapp, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oy0.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oy0.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 7oy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oy0_validation.pdf.gz | 970.6 KB | Display | wwPDB validaton report |
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Full document | 7oy0_full_validation.pdf.gz | 974.3 KB | Display | |
Data in XML | 7oy0_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 7oy0_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oy0 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oy0 | HTTPS FTP |
-Related structure data
Related structure data | 7oxlC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-6YU / |
#3: Chemical | ChemComp-3EI / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.01 M Na Acet, 0.06 M NaF |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.04 Å2 / Biso mean: 68.76 Å2 / Biso min: 23.82 Å2
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Refinement step | Cycle: final / Resolution: 2.09→167.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.095→2.149 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 70.706 Å / Origin y: -67.404 Å / Origin z: 19.717 Å
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Refinement TLS group |
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