+Open data
-Basic information
Entry | Database: PDB / ID: 7nb9 | ||||||
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Title | E. coli NfsA with nitrofurantoin | ||||||
Components | Oxygen-insensitive NADPH nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / complex with Antibiotic substrate / flavoprotein / nitroreductase | ||||||
Function / homology | Function and homology information chromate reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Day, M.D. / Jarrom, D. / Grainger, A.I. / Parr, R.J. / Hyde, E.I. / White, S.A. | ||||||
Citation | Journal: Biochem.J. / Year: 2021 Title: The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN. Authors: Day, M.A. / Jarrom, D. / Christofferson, A.J. / Graziano, A.E. / Anderson, J.L.R. / Searle, P.F. / Hyde, E.I. / White, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nb9.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nb9.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nb9_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 7nb9_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 7nb9_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 7nb9_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/7nb9 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/7nb9 | HTTPS FTP |
-Related structure data
Related structure data | 7niyC 7nmpC 7nnxC 1f5vS 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 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.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: nfsA, mda18, mdaA, ybjB, b0851, JW0835 / Plasmid: pPS1341A1 / Details (production host): pET24 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17117, Oxidoreductases |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-U6Z / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM imidazole pH 7, 20-26 % PEG 3,000, 3.5 mM nitrofurantoin, 20% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→45.69 Å / Num. obs: 83276 / % possible obs: 91.4 % / Redundancy: 3.4 % / Rsym value: 0.037 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.09→1.15 Å / Redundancy: 2.33 % / Mean I/σ(I) obs: 3.69 / Num. unique obs: 9425 / Rsym value: 0.22 / % possible all: 64.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F5V Resolution: 1.09→45.69 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.837 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 / 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: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.45 Å2 / Biso mean: 16.984 Å2 / Biso min: 7.11 Å2
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Refinement step | Cycle: final / Resolution: 1.09→45.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.09→1.119 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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