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Open data
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Basic information
Entry | Database: PDB / ID: 8qyg | ||||||
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Title | Crystal structure of Nitroreductase from Bacillus tequilensis | ||||||
![]() | NAD(P)H-dependent oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / FMN-binding | ||||||
Function / homology | Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / NAD(P)H-dependent oxidoreductase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rozeboom, H.J. / Russo, S. / Fraaije, M.W. / Poelarends, G.J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of Nitroreductase from Bacillus tequilensis Authors: Rozeboom, H.J. / Russo, S. / Fraaije, M.W. / Poelarends, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.3 KB | Display | ![]() |
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PDB format | ![]() | 182.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 39.4 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, 2 molecules AB
#1: Protein | Mass: 26401.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 670 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride, 20% PEG3350, MES buffer Ph 6.0 PH range: 5.9-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→46.5 Å / Num. obs: 157718 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.044 / Rrim(I) all: 0.088 / Χ2: 1.03 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.15→1.17 Å / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.575 / Num. measured all: 26982 / Num. unique obs: 7745 / CC1/2: 0.76 / Rpim(I) all: 0.354 / Rrim(I) all: 0.679 / Χ2: 0.83 / Net I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.002 Å2
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Refinement step | Cycle: 1 / Resolution: 1.15→46.5 Å
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Refine LS restraints |
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