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Yorodumi- PDB-1ooq: Nitroreductase from e-coli in complex with the inhibitor dicoumarol -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ooq | ||||||
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Title | Nitroreductase from e-coli in complex with the inhibitor dicoumarol | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / NAD(P)H-QUINONE REDUCTASE / FMN / NITROREDUCTASE / FLAVOPROTEIN / DICOUMAROL | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Johansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ooq.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ooq.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ooq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ooq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1ooq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1ooq_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1ooq_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/1ooq ftp://data.pdbj.org/pub/pdb/validation_reports/oo/1ooq | HTTPS FTP |
-Related structure data
Related structure data | 1idtC 1oo5C 1oo6C 1oonC 1ds7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P38489, 1.6.99.7 #2: Chemical | #3: Chemical | ChemComp-DTC / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |