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Open data
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Basic information
Entry | Database: PDB / ID: 1a2v | ||||||
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Title | COPPER AMINE OXIDASE FROM HANSENULA POLYMORPHA | ||||||
![]() | METHYLAMINE OXIDASE | ||||||
![]() | AMINE OXIDASE / QUINOPROTEIN / TOPAQUINONE ENZYME / TPQ | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Li, R. / Mathews, F.S. | ||||||
![]() | ![]() Title: Crystallographic study of yeast copper amine oxidase. Authors: Li, R. / Chen, L. / Cai, D. / 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 | ![]() | 806.6 KB | Display | ![]() |
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PDB format | ![]() | 669.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1oacS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 73690.047 Da / Num. of mol.: 6 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: 2.6 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 Details: PROTEIN WAS CRYSTALLIZED IN SITTING DROPS FROM 7-9% PEG 8000 AND 0.3 M POTASSIUM PHOSPHATE BUFFER, PH 6.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 172832 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.247 / % possible all: 66.8 |
Reflection shell | *PLUS % possible obs: 66.8 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() ![]() Starting model: PDB ENTRY 1OAC Resolution: 2.4→100 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 Details: BULK SOLVENT MODEL USED NCS RESTRAINTS. GROUP 1 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 1 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 1 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 1 B- ...Details: BULK SOLVENT MODEL USED NCS RESTRAINTS. GROUP 1 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 1 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 1 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 1 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 2 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 2 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 2 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 2 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 3 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 3 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 3 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 3 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 4 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 4 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 4 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 4 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 5 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 5 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 5 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 5 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 6 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 6 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 6 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 6 B-FACTOR MAIN CHAIN (A**2) : 4
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Displacement parameters | Biso mean: 24.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.279 |