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- PDB-2c12: Crystal Structure of Nitroalkane Oxidase in Complex with Spermine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c12 | ||||||
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Title | Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor | ||||||
![]() | NITROALKANE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOENZYME / NITROALKANE / ACYL-COA DEHYDROGENASE / LONG CELL EDGE / FAD / INHIBITOR / FLAVOPROTEIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 522.8 KB | Display | ![]() |
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PDB format | ![]() | 430.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 109 KB | Display | |
Data in CIF | ![]() | 147.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c0uSC 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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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1144 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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