+Open data
-Basic information
Entry | Database: PDB / ID: 1xpq | |||||||||
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Title | Crystal structure of fms1, a polyamine oxidase from yeast | |||||||||
Components | Polyamine oxidase FMS1 | |||||||||
Keywords | OXIDOREDUCTASE / polyamine oxidase / complex | |||||||||
Function / homology | Function and homology information non-specific polyamine oxidase / 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 / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / pantothenate biosynthetic process / flavin adenine dinucleotide binding ...non-specific polyamine oxidase / 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 / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / pantothenate biosynthetic process / flavin adenine dinucleotide binding / oxidoreductase activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | |||||||||
Authors | Huang, Q. / Liu, Q. / Hao, Q. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structures of Fms1 and its complex with spermine reveal substrate specificity. Authors: Huang, Q. / Liu, Q. / Hao, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xpq.cif.gz | 405.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xpq.ent.gz | 339.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/1xpq ftp://data.pdbj.org/pub/pdb/validation_reports/xp/1xpq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58529.148 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FMS1, YMR020W, YM9711.09 / Production host: Escherichia coli (E. coli) / References: UniProt: P50264, non-specific polyamine oxidase #2: Chemical | ChemComp-SPM / #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.627 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9474 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2004 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9474 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 82478 / Num. obs: 66331 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→42.93 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.78 Å2 / Biso mean: 49.4586 Å2 / Biso min: 17.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.51→42.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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