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Open data
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Basic information
Entry | Database: PDB / ID: 8spc | ||||||
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Title | Crystal structure of the cytochrome P450 enzyme RufO | ||||||
![]() | Cytochrome P450 | ||||||
![]() | METAL BINDING PROTEIN / RufO / Aromatic nitration / Cytochrome P450 | ||||||
Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dratch, B.D. / Davis, K.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into Substrate Recognition by the Unusual Nitrating Enzyme RufO. Authors: Dratch, B.D. / McWhorter, K.L. / Blue, T.C. / Jones, S.K. / Horwitz, S.M. / Davis, K.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 | ![]() | 104.8 KB | Display | ![]() |
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PDB format | ![]() | 69.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.7 KB | Display | ![]() |
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Full document | ![]() | 804.5 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45550.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 223 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % / Description: red, cube |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, 23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2022 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.871→39.34 Å / Num. obs: 35269 / % possible obs: 99.56 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.17 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09647 / Rpim(I) all: 0.02792 / Rrim(I) all: 0.1005 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 1.871→1.937 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 3398 / CC1/2: 0.687 / CC star: 0.903 / Rpim(I) all: 0.5285 / Rrim(I) all: 1.564 / % possible all: 96.32 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.871→39.34 Å
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Refine LS restraints |
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LS refinement shell |
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