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Yorodumi- PDB-2c12: Crystal Structure of Nitroalkane Oxidase in Complex with Spermine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c12 | ||||||
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Title | Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor | ||||||
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 / nitroethane oxidase activity / 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: 2.07 Å | ||||||
Authors | Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and Preliminary Analysis of Active Nitroalkane Oxidase in Three Crystal Forms Authors: Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. #2: Journal: Arch.Biochem.Biophys. / Year: 2005 Title: Nitroalkane Oxidase, a Carbanion-Forming Flavoprotein Homologous to Acyl-Coa Dehydrogenase Authors: Fitzpatrick, P.F. / Orville, A.M. / Nagpal, A. / Valley, M.P. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c12.cif.gz | 522.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c12.ent.gz | 430.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/2c12 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/2c12 | HTTPS FTP |
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-Related structure data
Related structure data | 2c0uSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 48219.246 Da / Num. of mol.: 6 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 |
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-Non-polymers , 5 types, 1144 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SPM / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | pH: 7.5 Details: 25%(W/V) PEG 4000, 35% (V/V) GLYCEROL, 200 MM SODIUM CACODYLATE TRIHYDRATE PH 7.5, 1 MM SPERMINE TETRAHYDROCHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 180533 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 1.64 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.07→2.15 Å / Redundancy: 1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C0U Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.182 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.169 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→50 Å
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Refine LS restraints |
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