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- PDB-5b1k: Crystal structure of the chloride-bound form of blue copper nitri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b1k | ||||||
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Title | Crystal structure of the chloride-bound form of blue copper nitrite reductase | ||||||
![]() | Copper-containing nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / copper nitrite reductase / chloride ion | ||||||
Function / homology | ![]() denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / nitrate assimilation / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nojiri, M. | ||||||
![]() | ![]() Journal: Metalloenzymes in denitrification: Applications and Environmental impacts Year: 2016 Title: Structure and function of copper nitrite reductase Authors: Nojiri, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.8 KB | Display | ![]() |
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PDB format | ![]() | 122.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.9 KB | Display | ![]() |
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Full document | ![]() | 429 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 36667.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nir, nirK, ERS451415_02178 / Plasmid: pET23c / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.81 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / Details: PEG 3350, Sodium Chloride, Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Jan 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→90.5 Å / Num. obs: 86291 / % possible obs: 99.9 % / Redundancy: 5.2 % / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
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Processing
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Refinement | Resolution: 1.35→90.5 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.856 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.897 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→90.5 Å
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Refine LS restraints |
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