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Yorodumi- PDB-5lgb: Crystal structure of murine N1-acetylpolyamine oxidase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lgb | ||||||
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Title | Crystal structure of murine N1-acetylpolyamine oxidase in complex with MDL72527 | ||||||
Components | Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase | ||||||
Keywords | OXIDOREDUCTASE / flavin amine oxidase | ||||||
Function / homology | Function and homology information N1-acetylpolyamine oxidase / N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity / N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / spermine:oxygen oxidoreductase (spermidine-forming) activity ...N1-acetylpolyamine oxidase / N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity / N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / spermine:oxygen oxidoreductase (spermidine-forming) activity / putrescine catabolic process / polyamine oxidase activity / spermidine catabolic process / spermine catabolic process / polyamine catabolic process / Peroxisomal protein import / peroxisomal matrix Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sjogren, T. / Aagaard, A. / Wassvik, C. / Snijder, A. / Barlind, L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lgb.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lgb.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/5lgb ftp://data.pdbj.org/pub/pdb/validation_reports/lg/5lgb | HTTPS FTP |
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-Related structure data
Related structure data | 5laeSC 5lfoC 5mbxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-6YU / |
#3: Chemical | ChemComp-MD2 / |
#4: 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: 2.13 Å3/Da / Density % sol: 42.29 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.8→1.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso mean: 39.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→40.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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