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Yorodumi- PDB-7t33: The structure of Haemophilus influenzae Rd KW20 nitroreductase co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t33 | ||||||
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Title | The structure of Haemophilus influenzae Rd KW20 nitroreductase complexed with nicotinic acid | ||||||
Components | Putative NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / Nitroreductase Haemophilus influenzae Nicotinic acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae Rd KW20 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å | ||||||
Authors | Wanniarachchi, T.N. / Bruner, S.D. | ||||||
Funding support | 1items
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Citation | Journal: Rsc Chem Biol / Year: 2022 Title: Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles. Authors: Liu, D. / Wanniarachchi, T.N. / Jiang, G. / Seabra, G. / Cao, S. / Bruner, S.D. / Ding, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t33.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t33.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 7t33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/7t33 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/7t33 | HTTPS FTP |
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-Related structure data
Related structure data | 7t2zC 6wt2S C: citing same article (ref.) S: Starting model for refinement |
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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: 26747.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57431, Oxidoreductases #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: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.4476 Å / Num. obs: 19464 / % possible obs: 99.13 % / Redundancy: 9.4 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 19.15 |
Reflection shell | Resolution: 2.301→2.384 Å / Redundancy: 5.2 % / Num. unique obs: 1838 / CC1/2: 0.807 / CC star: 0.945 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WT2 Resolution: 2.301→49.4476 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.51 Å2 / Biso mean: 55.1389 Å2 / Biso min: 30.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→49.4476 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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