[English] 日本語
Yorodumi- PDB-1b37: A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b37 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE OF POLYAMINE OXIDASE | |||||||||
Components | PROTEIN (POLYAMINE OXIDASE) | |||||||||
Keywords | OXIDOREDUCTASE / FLAVIN-DEPENDENT AMINE OXIDASE | |||||||||
Function / homology | Function and homology information polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / spermidine oxidase (propane-1,3-diamine-forming) activity / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / plant-type cell wall / polyamine catabolic process ...polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / spermidine oxidase (propane-1,3-diamine-forming) activity / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / plant-type cell wall / polyamine catabolic process / apoplast / peroxisome / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | |||||||||
Authors | Binda, C. / Coda, A. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. Authors: Binda, C. / Coda, A. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1b37.cif.gz | 307.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1b37.ent.gz | 246.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b37_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1b37_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1b37_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 1b37_validation.cif.gz | 84.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b37 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b37 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
5 |
| ||||||||||||
6 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 53698.457 Da / Num. of mol.: 3 / Fragment: FAD-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: O64411, EC: 1.5.3.11 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.5 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 216570 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 |
Reflection | *PLUS Num. measured all: 785004 |
Reflection shell | *PLUS % possible obs: 88.4 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.234 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.015 |