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Yorodumi- PDB-7uwt: Structure of Oxygen-Insensitive NAD(P)H-dependent Nitroreductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uwt | ||||||||||||
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Title | Structure of Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB_Vv F70A/F108Y (NTR 2.0) in complex with FMN at 1.85 Angstroms resolution | ||||||||||||
Components | Dihydropteridine reductase6,7-dihydropteridine reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / nitroreductase / flavoenzyme / metronidazole reductase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||||||||
Authors | Sharrock, A.V. / Arcus, V. / Mumm, J.S. / Ackerley, D.F. | ||||||||||||
Funding support | United States, New Zealand, 3items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Substitutions on Substrate Specificity. Authors: Sharrock, A.V. / Mumm, J.S. / Bagdziunas, G. / Cenas, N. / Arcus, V.L. / Ackerley, D.F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uwt.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uwt.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 7uwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uwt ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uwt | HTTPS FTP |
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-Related structure data
Related structure data | 1ds7S S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24149.348 Da / Num. of mol.: 2 / Mutation: F70A,F108Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: FORC53_4366, JS85_12320 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A347SKZ6, 6,7-dihydropteridine reductase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate trihydrate pH 4.5, PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→68.68 Å / Num. obs: 43344 / % possible obs: 99.9 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2625 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DS7 Resolution: 1.85→68.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.457 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.826 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→68.68 Å
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