+Open data
-Basic information
Entry | Database: PDB / ID: 1ds7 | ||||||
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Title | A MINOR FMN-DEPENDENT NITROREDUCTASE FROM ESCHERICHIA COLI B | ||||||
Components | FMN-DEPENDENT NITROREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NAD(P)H-QUINONE REDUCTASE / FMN / NITROREDUCTASE / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information : / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.06 Å | ||||||
Authors | Parkinson, G. / Skelly, J. / Neidle, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2000 Title: Crystal structure of FMN-dependent nitroreductase from Escherichia coli B: a prodrug-activating enzyme. Authors: Parkinson, G.N. / Skelly, J.V. / Neidle, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ds7.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ds7.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ds7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/1ds7 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/1ds7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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) / Strain: B / Plasmid: PK12 / Production host: Escherichia coli (E. coli) / References: UniProt: P38489, 1.6.99.7 #2: Chemical | #3: 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: 2.4 Å3/Da / Density % sol: 48.7 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Peg 8000, potassium phosphate, NaCl, pH 7.0, 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: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1993 / Details: MIRROR |
Radiation | Monochromator: N / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 23317 / % possible obs: 71.3 % / Biso Wilson estimate: 4 Å2 / Rmerge(I) obs: 0.114 |
Reflection | *PLUS Highest resolution: 1.85 Å / Num. obs: 24109 / % possible obs: 81 % / Num. measured all: 127222 / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Resolution: 2.06→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 294380.81 / 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: 22.24 Å2 / ksol: 0.277 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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