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- PDB-8rur: High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rur | |||||||||
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Title | High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.38 MGy] | |||||||||
![]() | Copper-containing nitrite reductase | |||||||||
![]() | OXIDOREDUCTASE / electron transfer / Nitrite binding / nitrite reductase | |||||||||
Function / homology | ![]() denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, A.L. / Antonyuk, S.V. / Hasnain, S.S. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases. Authors: Rose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Hasnain, S.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.1 KB | Display | ![]() |
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PDB format | ![]() | 244.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r8sC ![]() 8rflC ![]() 8rfoC ![]() 8rfpC ![]() 8rfqC ![]() 8rfrC ![]() 8rfsC ![]() 8rftC ![]() 8rfuC ![]() 8rfvC ![]() 8rfwC ![]() 8rfxC ![]() 8rfyC ![]() 8rg8C ![]() 8rg9C ![]() 8rgbC ![]() 8rgcC ![]() 8rgdC ![]() 8ru9C ![]() 8ryjC ![]() 8ryrC ![]() 8ryuC ![]() 8ryvC ![]() 8s0wC ![]() 8s2qC ![]() 8s5xC ![]() 8s5yC ![]() 8s63C ![]() 8s64C ![]() 8s68C ![]() 8s69C ![]() 9evmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 39758.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose |
-Non-polymers , 4 types, 510 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-NO2 / | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate |
-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: Feb 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→45.039 Å / Num. obs: 146809 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.038 / Rrim(I) all: 0.087 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.13→1.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7207 / CC1/2: 0.449 / Rpim(I) all: 0.575 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been used if present in the input file
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.997 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→45.004 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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