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Open data
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Basic information
Entry | Database: PDB / ID: 7q0o | ||||||
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Title | E. coli NfsA | ||||||
![]() | Oxygen-insensitive NADPH nitroreductase | ||||||
![]() | OXIDOREDUCTASE / Oxygen-insensitive NADPH nitroreductase | ||||||
Function / homology | ![]() chromate reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | White, S.A. / Grainger, A. / Parr, R. / Day, M.A. / Jarrom, D. / Graziano, A. / Searle, P.F. / Hyde, E.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The 3D-structure, kinetics and dynamics of the E. coli nitroreductase NfsA with NADP + provide glimpses of its catalytic mechanism. Authors: White, S.A. / Christofferson, A.J. / Grainger, A.I. / Day, M.A. / Jarrom, D. / Graziano, A.E. / Searle, P.F. / Hyde, E.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.8 KB | Display | ![]() |
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PDB format | ![]() | 97.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 834.5 KB | Display | ![]() |
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Full document | ![]() | 834.5 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z0wC ![]() 1f5vS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 26832.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 100 mM imidazole, pH 7.6, 20% PEG 6000, 200 mM Magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→41.28 Å / Num. obs: 132860 / % possible obs: 96.31 % / Redundancy: 1.8 % / Biso Wilson estimate: 10.82 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0217 / Rpim(I) all: 0.0217 / Rrim(I) all: 0.03069 / Net I/σ(I): 16.71 |
Reflection shell | Resolution: 0.96→0.9943 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.2251 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 10998 / CC1/2: 0.901 / CC star: 0.974 / Rpim(I) all: 0.2251 / Rrim(I) all: 0.3184 / % possible all: 79.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F5V Resolution: 0.96→41.28 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.605 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 229.52 Å2 / Biso mean: 19.105 Å2 / Biso min: 7.67 Å2
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Refinement step | Cycle: final / Resolution: 0.96→41.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.96→0.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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