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- PDB-5ofh: Cu nitrite reductase serial data at varying temperatures RT 0.15MGy -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ofh | ||||||||||||
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Title | Cu nitrite reductase serial data at varying temperatures RT 0.15MGy | ||||||||||||
![]() | 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 | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5of5C ![]() 5of6C ![]() 5of7C ![]() 5of8C ![]() 5ofcC ![]() 5ofdC ![]() 5ofeC ![]() 5offC ![]() 5ofgC ![]() 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
#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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#2: Chemical | #3: Chemical | ChemComp-NO2 / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.36 % |
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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: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→48.12 Å / Num. obs: 40744 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.079 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.54 / Rpim(I) all: 0.533 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I6K Resolution: 1.58→48.12 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.94 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077
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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: 22.211 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→48.12 Å
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Refine LS restraints |
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