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Open data
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Basic information
Entry | Database: PDB / ID: 5of5 | ||||||||||||
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Title | Cu nitrite reductase serial data at varying temperatures | ||||||||||||
![]() | Copper-containing nitrite reductase | ||||||||||||
![]() | OXIDOREDUCTASE / Electron transfer / 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 | ![]() ![]() ![]() | ||||||||||||
![]() | Horrell, S. / Kekilli, D. / Strange, R.W. / Hough, M.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Enzyme catalysis captured using multiple structures from one crystal at varying temperatures. Authors: Horrell, S. / Kekilli, D. / Sen, K. / Owen, R.L. / Dworkowski, F.S.N. / Antonyuk, S.V. / Keal, T.W. / Yong, C.W. / Eady, R.R. / Hasnain, S.S. / Strange, R.W. / Hough, M.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.2 KB | Display | ![]() |
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PDB format | ![]() | 131.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5of6C ![]() 5of7C ![]() 5of8C ![]() 5ofcC ![]() 5ofdC ![]() 5ofeC ![]() 5offC ![]() 5ofgC ![]() 5ofhC ![]() 5og2C ![]() 5og3C ![]() 5og4C ![]() 5og5C ![]() 5og6C ![]() 5ogfC ![]() 5oggC ![]() 5i6kS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36621.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 453 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NO2 / #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-MLI / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM sodium citrate at pH 5.0 and ~1.7 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→42.46 Å / Num. obs: 120835 / % possible obs: 99.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 8 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.029 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.32 / Rpim(I) all: 0.623 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I6K Resolution: 1.08→42.46 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.968 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.26 Å2
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Refinement step | Cycle: 1 / Resolution: 1.08→42.46 Å
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Refine LS restraints |
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