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Yorodumi- PDB-1b5q: A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b5q | |||||||||
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b5q.cif.gz | 306.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b5q.ent.gz | 246.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b5q_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1b5q_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1b5q_validation.xml.gz | 60.5 KB | Display | |
Data in CIF | 1b5q_validation.cif.gz | 84.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/1b5q ftp://data.pdbj.org/pub/pdb/validation_reports/b5/1b5q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#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: GenBank: CAA05249, UniProt: O64411*PLUS |
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-Sugars , 2 types, 3 molecules
#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 |
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-Non-polymers , 3 types, 634 molecules
#4: Chemical | #5: Chemical | #6: 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: 4.3 Å3/Da / Density % sol: 71.37 % | ||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
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. obs: 211025 / % possible obs: 96.6 % / Num. measured all: 704940 / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 100 Å / σ(F): 0 / Num. reflection Rfree: 2125 / % reflection Rfree: 1 % / Rfactor all: 0.193 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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