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- PDB-3d9d: Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d9d | ||||||
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Title | Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane | ||||||
![]() | Nitroalkane oxidase | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE FLAVOENZYME / NITROALKANE / ACYL-COA DEHYDROGENASE / LONG CELL EDGE / FAD / INHIBITOR / FLAVOPROTEIN | ||||||
Function / homology | ![]() nitroalkane oxidase activity / nitroalkane oxidase / : / butyrate catabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / : / oxidoreductase activity, acting on the CH-CH group of donors / FAD binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Heroux, A. / Bozinovski, D.M. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. | ||||||
![]() | ![]() Title: Crystal structures of intermediates in the nitroalkane oxidase reaction. Authors: Heroux, A. / Bozinovski, D.M. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. #1: ![]() Title: Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover. Authors: Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. #2: ![]() Title: Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase. Authors: Fitzpatrick, P.F. / Bozinovski, D.M. / Heroux, A. / Shaw, P.G. / Valley, M.P. / Orville, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347.3 KB | Display | ![]() |
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PDB format | ![]() | 283.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 68.4 KB | Display | |
Data in CIF | ![]() | 94.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d9eC ![]() 3d9fC ![]() 3d9gC ![]() 2c12S 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: 48087.066 Da / Num. of mol.: 4 / Mutation: D402N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-N6C / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-30mM PEG 3350, 20-35% glycerol, 0.1M NaCacodylate, pH 7.50, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 391270 / Num. obs: 391270 / % possible obs: 91.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 13.72 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.2 / Num. unique all: 8209 / Rsym value: 0.447 / % possible all: 62.1 |
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Processing
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Refinement | Method to determine structure: MOLREP Starting model: 2c12 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.337 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.192 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.174 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.156 Å / Total num. of bins used: 20
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