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- PDB-7zcp: Nitrite-bound MSOX movie series dataset 17 (13.6 MGy) of the copp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zcp | |||||||||
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Title | Nitrite-bound MSOX movie series dataset 17 (13.6 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - nitric oxide (NO) intermediate | |||||||||
![]() | Copper-containing nitrite reductase | |||||||||
![]() | OXIDOREDUCTASE / Nitrite reductase / Copper nitrite reductase / Copper-containing nitrite reductase / BrNiR / Br2DNiR / nitrite-bound / MSOX | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Rose, S.L. / Baba, S. / Okumura, H. / Antonyuk, S.V. / Sasaki, D. / Tosha, T. / Kumasaka, T. / Eady, R.R. / Yamamoto, M. / Hasnain, S.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases. Authors: Rose, S.L. / Baba, S. / Okumura, H. / Antonyuk, S.V. / Sasaki, D. / Hedison, T.M. / Shanmugam, M. / Heyes, D.J. / Scrutton, N.S. / Kumasaka, T. / Tosha, T. / Eady, R.R. / Yamamoto, M. / Hasnain, S.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189 KB | Display | ![]() |
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PDB format | ![]() | 149 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qxkC ![]() 7qy4C ![]() 7qycC ![]() 7zcnC ![]() 7zcoSC ![]() 7zcqC ![]() 7zcrC ![]() 7zcsC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 38288.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide |
-Non-polymers , 6 types, 548 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NO / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→75.65 Å / Num. obs: 112299 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 11.05 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.041 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 5613 / CC1/2: 0.339 / Rpim(I) all: 0.816 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ZCO Resolution: 1.29→75.65 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.981 / SU B: 2.916 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / 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: 18.794 Å2
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Refinement step | Cycle: 1 / Resolution: 1.29→75.65 Å
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Refine LS restraints |
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