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- PDB-7t33: The structure of Haemophilus influenzae Rd KW20 nitroreductase co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t33 | ||||||
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Title | The structure of Haemophilus influenzae Rd KW20 nitroreductase complexed with nicotinic acid | ||||||
![]() | Putative NAD(P)H nitroreductase | ||||||
![]() | OXIDOREDUCTASE / Nitroreductase Haemophilus influenzae Nicotinic acid | ||||||
Function / homology | ![]() oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wanniarachchi, T.N. / Bruner, S.D. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.6 KB | Display | ![]() |
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PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t2zC ![]() 6wt2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1278 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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