+Open data
-Basic information
Entry | Database: PDB / ID: 1rsg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the polyamine oxidase Fms1 from yeast | ||||||
Components | FMS1 protein | ||||||
Keywords | OXIDOREDUCTASE / FAD binding motif | ||||||
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 / SAD / Resolution: 1.9 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. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 2003 Title: Yeast Fms1 is a FAD-utilizing polyamine oxidase Authors: Landry, J. / Sternglanz, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rsg.cif.gz | 225.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rsg.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 1rsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/1rsg ftp://data.pdbj.org/pub/pdb/validation_reports/rs/1rsg | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 59506.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FMS1, YMR020W, YM9711.09 / Plasmid: pET28 / 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 3350, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 31, 2003 | |||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.9→40 Å / Num. all: 100168 / Num. obs: 96862 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.051 | |||||||||||||||
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.302 / Num. unique all: 3607 / % possible all: 73 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.9→35.95 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35.95 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009
|