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- PDB-3n9h: Crystal Structural of mutant Y305A in the copper amine oxidase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n9h | ||||||
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Title | Crystal Structural of mutant Y305A in the copper amine oxidase from hansenula polymorpha | ||||||
![]() | Peroxisomal primary amine oxidase | ||||||
![]() | OXIDOREDUCTASE / amine oxidase / quinoprotein | ||||||
Function / homology | ![]() primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / peroxisome / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Z. / Datta, S. / DuBois, J.L. / Klinman, J.P. / Mathews, F.S. | ||||||
![]() | ![]() Title: Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity. Authors: Chen, Z.W. / Datta, S. / Dubois, J.L. / Klinman, J.P. / Mathews, F.S. #1: Journal: Structure / Year: 1998 Title: Copper amine oxidase from Hansenula polymorpha: the crystal structure determined at 2.4 A resolution reveals the active conformation. Authors: Li, R. / Klinman, J.P. / Mathews, F.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 815.3 KB | Display | ![]() |
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PDB format | ![]() | 676.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.1 KB | Display | ![]() |
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Full document | ![]() | 589.7 KB | Display | |
Data in XML | ![]() | 174.9 KB | Display | |
Data in CIF | ![]() | 252 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nbbC ![]() 3nbjC ![]() 1a2vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 77570.508 Da / Num. of mol.: 6 / Mutation: Y305A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.08 % |
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Crystal grow | Temperature: 295 K / pH: 6.3 Details: 10% PEG8000. 0.125M Lithium sulfate and 0.1M KPi, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2000 |
Radiation | Monochromator: APS BEAMLINE 19-ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30.1 Å / Num. obs: 134330 / % possible obs: 79.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.1 / % possible all: 41 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A2V Resolution: 2.5→30.1 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 29.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å
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