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- PDB-3nbj: Crystal Structure of Y305F mutant of the copper amine oxidase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nbj | ||||||
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Title | Crystal Structure of Y305F mutant of the copper amine oxidase from Hansenula polymorpha expressed in yeast | ||||||
![]() | 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 | ![]() | 814.4 KB | Display | ![]() |
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PDB format | ![]() | 675.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 513.6 KB | Display | ![]() |
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Full document | ![]() | 601.4 KB | Display | |
Data in XML | ![]() | 170.4 KB | Display | |
Data in CIF | ![]() | 240.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n9hC ![]() 3nbbC ![]() 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 77696.617 Da / Num. of mol.: 6 / Mutation: Y305F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 8% PEG8000, 200mM KPi, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 358174 / Num. obs: 313044 / % possible obs: 87.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.2 / % possible all: 53.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A2V Resolution: 1.9→29.88 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 524478.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.2 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep_tpo405.par / Topol file: protein_tpo405.top |