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- PDB-2zaf: Mechanistic and Structural Analyses of the Roles of Arg409 and As... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zaf | ||||||
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Title | Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase | ||||||
![]() | Nitroalkane oxidase | ||||||
![]() | OXIDOREDUCTASE / FLAVOENZYME / NITROALKANE / 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 | ![]() ![]() | ||||||
![]() | Fitzpatrick, P.F. / Bozinovski, D.M. / Heroux, A. / Shaw, P.G. / Valley, M.P. / Orville, A.M. | ||||||
![]() | ![]() 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. #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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.4 KB | Display | ![]() |
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PDB format | ![]() | 267.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 59.4 KB | Display | |
Data in CIF | ![]() | 78.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rehC ![]() 1c0uS C: citing same article ( 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 domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 431 / Label seq-ID: 2 - 431
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Components
#1: Protein | Mass: 48191.230 Da / Num. of mol.: 4 / Mutation: R409K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25-30%(W/V) PEG 3350, 35% (V/V) GLYCEROL, 200MM SODIUM CACODYLATE TRIHYDRATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2006 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 81166 / Num. obs: 81166 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.128 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.5→2.74 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.587 / % possible all: 93.2 |
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Processing
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Refinement | Starting model: 1c0u Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.771 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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