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- PDB-5i6l: Crystal Structure of Copper Nitrite Reductase at 100K after 2.76 MGy -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i6l | |||||||||
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Title | Crystal Structure of Copper Nitrite Reductase at 100K after 2.76 MGy | |||||||||
![]() | Copper-containing nitrite reductase | |||||||||
![]() | OXIDOREDUCTASE / Copper Nitrite Reductase / Reaction Mechanism / Serial Crystallography | |||||||||
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. / Hough, M.A. / Strange, R.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal. Authors: Horrell, S. / Antonyuk, S.V. / Eady, R.R. / Hasnain, S.S. / Hough, M.A. / Strange, R.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.2 KB | Display | ![]() |
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PDB format | ![]() | 128.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i6kC ![]() 5i6mC ![]() 5i6nC ![]() 5i6oC ![]() 5i6pC ![]() 2bwiS 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: 36391.008 Da / Num. of mol.: 1 / Fragment: Copper Nitrite Reductase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 355 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-MLI / | #5: Chemical | ChemComp-NO2 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.99 % / Mosaicity: 0.17 ° |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.5 Details: 1.7 M Ammonium Sulphate, 0.1 M Sodium Acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.08→42.62 Å / Num. obs: 119248 / % possible obs: 97.4 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.024 / Rrim(I) all: 0.052 / Net I/σ(I): 14.8 / Num. measured all: 477406 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BWI Resolution: 1.08→42.61 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.864 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 94.09 Å2 / Biso mean: 14.165 Å2 / Biso min: 5.87 Å2
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Refinement step | Cycle: final / Resolution: 1.08→42.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.08→1.108 Å / Total num. of bins used: 20
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