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Yorodumi- PDB-3d9f: Nitroalkane oxidase: active site mutant S276A crystallized with 1... -
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-Basic information
Entry | Database: PDB / ID: 3d9f | ||||||
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Title | Nitroalkane oxidase: active site mutant S276A crystallized with 1-nitrohexane | ||||||
Components | Nitroalkane oxidase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / NITROALKANE / ACYL-COA DEHYDROGENASE / LONG CELL EDGE / FAD / INHIBITOR / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information 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 | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Heroux, A. / Bozinovski, D.M. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 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: Journal: Biochemistry / Year: 2006 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: Journal: Biochemistry / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d9f.cif.gz | 341.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d9f.ent.gz | 279.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d9f_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3d9f_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3d9f_validation.xml.gz | 66.6 KB | Display | |
Data in CIF | 3d9f_validation.cif.gz | 91 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d9f ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d9f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48072.051 Da / Num. of mol.: 4 / Mutation: S276A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PETNAO4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q8X1D8, nitroalkane oxidase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 % |
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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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2007 |
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: 2.2→50 Å / Num. obs: 115243 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 43.94 Å2 / Rsym value: 0.069 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / Num. unique all: 9698 / Rsym value: 0.552 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.781 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.194 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.946 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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