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- PDB-1d6y: CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d6y | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE AND COMPLEXED WITH NITRIC OXIDE. | ||||||
![]() | COPPER AMINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / REACTION INTERMEDIATE MIMIC | ||||||
Function / homology | ![]() phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wilmot, C.M. / Hajdu, J. / McPherson, M.J. / Knowles, P.F. / Phillips, S.E.V. | ||||||
![]() | ![]() Title: Visualization of dioxygen bound to copper during enzyme catalysis. Authors: Wilmot, C.M. / Hajdu, J. / McPherson, M.J. / Knowles, P.F. / Phillips, S.E. #1: ![]() Title: The Active Site Base Controls Cofactor Reactivity in Escherichia coli Amine Oxidase: X-ray Crystallographic Studies with Mutational Variants. Authors: Murray, J.M. / Saysell, C.G. / Wilmot, C.M. / Tambyrajah, W.S. / Jaeger, J. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J. #2: ![]() Title: Catalytic Mechanism of the Quinoenzyme Amine Oxidase from Escherichia coli: Exploring the Reductive Half-Reaction. Authors: Wilmot, C.M. / Murray, J.M. / Alton, G. / Parsons, M.R. / Convery, M.A. / Blakeley, V. / Corner, A.S. / Palcic, M.M. / Knowles, P.F. / McPherson, M.J. / Knowles, P.F. #3: ![]() Title: Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia coli at 2 Angstroms Resolution. Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D.S. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327 KB | Display | ![]() |
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PDB format | ![]() | 261 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 81367.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 1440 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HY1.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/PEA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HY1.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/PEA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEA / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % | |||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: sodium citrate, HEPES buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 18K | |||||||||||||||
Crystal | *PLUS Density % sol: 55 % | |||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 65769 / Num. obs: 191118 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.265 / % possible all: 92.5 |
Reflection | *PLUS Num. obs: 65769 / Num. measured all: 191118 |
Reflection shell | *PLUS % possible obs: 92.5 % |
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Processing
Software |
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Refinement | Resolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |