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Open data
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Basic information
Entry | Database: PDB / ID: 6p5q | ||||||
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Title | X-ray structure of Fe(II)-soaked UndA bound to lauric acid | ||||||
![]() | UndA | ||||||
![]() | OXIDOREDUCTASE / desaturase / iron / decarboxylase / fatty acid | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rajakovich, L.J. / Mitchell, A.J. / Boal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate-Triggered Formation of a Peroxo-Fe2(III/III) Intermediate during Fatty Acid Decarboxylation by UndA. Authors: Zhang, B. / Rajakovich, L.J. / Van Cura, D. / Blaesi, E.J. / Mitchell, A.J. / Tysoe, C.R. / Zhu, X. / Streit, B.R. / Rui, Z. / Zhang, W. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.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 | ![]() | 252 KB | Display | ![]() |
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PDB format | ![]() | 165.5 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 | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wwjS 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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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35177.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-FE / #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: 3.16 Å3/Da / Density % sol: 61.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→34 Å / Num. obs: 61998 / % possible obs: 98.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.86→1.89 Å / Rmerge(I) obs: 0.469 / Num. unique obs: 3070 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WWJ Resolution: 1.86→33.08 Å / SU ML: 0.1859 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5952 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→33.08 Å
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Refine LS restraints |
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LS refinement shell |
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