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- PDB-1oo5: Studies on the Nitroreductase Prodrug-Activating System. Crystal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oo5 | ||||||
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Title | Studies on the Nitroreductase Prodrug-Activating System. Crystal Structures of the Enzyme Active Form and Complexes with the Inhibitor Dicoumarol and Dinitrobenzamide Prodrugs | ||||||
![]() | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
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Function / homology | ![]() oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 75.2 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 ![]() 1oo6C ![]() 1oonC ![]() 1ooqC ![]() 1ds7S C: citing same article ( 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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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: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.7 % |
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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 |
-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001 |
Radiation | Monochromator: diamond (111) germanium (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→20 Å / Num. all: 15515 / Num. obs: 15515 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10 |
Reflection shell | Highest resolution: 2.5 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 1 / Num. unique all: 1402 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1DS7 Resolution: 2.5→19.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 161733.98 / Data cutoff high rms absF: 161733.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.4561 Å2 / ksol: 0.320748 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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