+Open data
-Basic information
Entry | Database: PDB / ID: 3cn8 | ||||||
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Title | Crystal structure of fms1 in complex with spermidine | ||||||
Components | Polyamine oxidase FMS1 | ||||||
Keywords | OXIDOREDUCTASE / fms1 / complex / spermidine / FAD / Flavoprotein | ||||||
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 / Resolution: 2.4 Å | ||||||
Authors | Huang, Q. / Hao, Q. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of fms1 in complex with spermidine Authors: Huang, 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 | 3cn8.cif.gz | 209.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cn8.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cn8 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cn8 | HTTPS FTP |
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-Related structure data
Related structure data | 1yy5S S: Starting model for refinement |
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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: 58943.594 Da / Num. of mol.: 2 / Fragment: fms1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FMS1 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50264, EC: 1.5.3.11 #2: Chemical | #3: Chemical | #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: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG8000, 0.2M Li2SO4, 0.1M Tris-HCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9779 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2007 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 67178 / Num. obs: 62677 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.076 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3314 / Rsym value: 0.581 / % possible all: 81.6 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1YY5 Resolution: 2.4→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 54.481 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.682 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.31 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014
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Xplor file |
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