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- PDB-1ooq: Nitroreductase from e-coli in complex with the inhibitor dicoumarol -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ooq | ||||||
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Title | Nitroreductase from e-coli in complex with the inhibitor dicoumarol | ||||||
![]() | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
![]() | OXIDOREDUCTASE / NAD(P)H-QUINONE REDUCTASE / FMN / NITROREDUCTASE / FLAVOPROTEIN / DICOUMAROL | ||||||
Function / homology | ![]() oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 6,7-dihydropteridine reductase / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S. | ||||||
![]() | ![]() Title: Studies on the Nitroreductase Prodrug-Activating System. Crystal Structures of Complexes with the Inhibitor Dicoumarol and Dinitrobenzamide Prodrugs and of the Enzyme Active Form Authors: Johansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1idtC ![]() 1oo5C ![]() 1oo6C ![]() 1oonC ![]() 1ds7S 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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Unit cell |
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Components
#1: Protein | Mass: 23937.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DTC / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.34 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000 (25%-29%), 0.1 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 2001 |
Radiation | Monochromator: germanium 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 22217 / Num. obs: 22217 / % possible obs: 69.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 12 / Num. unique all: 2504 / % possible all: 80.8 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 70 % / Num. measured all: 31904 |
Reflection shell | *PLUS % possible obs: 82.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DS7 Resolution: 2→19.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 436534.2 / Data cutoff high rms absF: 436534.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.273883 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å |