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- PDB-5n8g: Serial Cu nitrite reductase structures at elevated cryogenic temp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n8g | |||||||||
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Title | Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 2. | |||||||||
![]() | Copper-containing nitrite reductase | |||||||||
![]() | OXIDOREDUCTASE / nitrite reductase / copper enzyme / trimer / cupredoxid domain | |||||||||
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. / Hough, M. / Strange, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase. Authors: Sen, K. / Horrell, S. / Kekilli, D. / Yong, C.W. / Keal, T.W. / Atakisi, H. / Moreau, D.W. / Thorne, R.E. / 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 | ![]() | 89.2 KB | Display | ![]() |
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PDB format | ![]() | 65 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.8 KB | Display | ![]() |
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Full document | ![]() | 435.8 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n8fC ![]() 5n8hC ![]() 5n8iC ![]() 2bw4S 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-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium citrate at pH 5.0 and 1.6 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 240 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→28.99 Å / Num. obs: 50265 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2473 / CC1/2: 0.513 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BW4 Resolution: 1.47→28.99 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.232 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / 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: 14.91 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→28.99 Å
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Refine LS restraints |
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