+Open data
-Basic information
Entry | Database: PDB / ID: 8c5e | ||||||
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Title | E. coli NfsB-T41Q/N71S/F124T mutant bound to nicotinic acid | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / Nitroreductase mutant / complex | ||||||
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: 1.65 Å | ||||||
Authors | White, S.A. / Hyde, E.I. / Day, M.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structure and Dynamics of Three Escherichia coli NfsB Nitro-Reductase Mutants Selected for Enhanced Activity with the Cancer Prodrug CB1954. Authors: Day, M.A. / Christofferson, A.J. / Anderson, J.L.R. / Vass, S.O. / Evans, A. / Searle, P.F. / White, S.A. / Hyde, E.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5e.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5e.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 8c5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c5e_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8c5e_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8c5e_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 8c5e_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5e ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5e | HTTPS FTP |
-Related structure data
Related structure data | 8c5fC 8c5pC 8ccvC 8cj0C 8og3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 23759.916 Da / Num. of mol.: 2 / Mutation: T41Q, N71S, F124T Source method: isolated from a genetically manipulated source Details: Triple mutant of NfsB, bound to nicotinate / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5a / Gene: nfsB, dprA, nfnB, nfsI, ntr, b0578, JW0567 / Plasmid: pET11c / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P38489, Oxidoreductases, 6,7-dihydropteridine reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, 50-200 mM sodium acetate buffer, 15 mM nicotinic acid, 15% ethylene glycol |
-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: MAR CCD 165 mm / 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: 1.65→48.24 Å / Num. obs: 53617 / % possible obs: 97.7 % / Redundancy: 5.42 % / Rsym value: 0.078 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.79 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6747 / Rsym value: 0.557 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.5 Å / SU B: 4.056 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 13.041 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→43.5 Å
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LS refinement shell | Resolution: 1.653→1.696 Å
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