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- PDB-4ysr: Structure of copper nitrite reductase from Geobacillus thermodeni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ysr | ||||||
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Title | Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.6 MGy | ||||||
![]() | Nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / Nitrite / Copper / Reductase | ||||||
Function / homology | ![]() nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. ...Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Matsumura, H. / Inoue, T. / Iwata, S. / Mizohata, E. | ||||||
![]() | ![]() Title: Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography Authors: Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / ...Authors: Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Matsumura, H. / Inoue, T. / Iwata, S. / Mizohata, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145 KB | Display | ![]() |
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PDB format | ![]() | 112.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.1 KB | Display | ![]() |
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Full document | ![]() | 450.7 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ysaC ![]() 4ysdC ![]() 4ysoC ![]() 4yspC ![]() 4ysqC ![]() 4yssC ![]() 4ystC ![]() 4ysuC 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
#1: Protein | Mass: 35523.062 Da / Num. of mol.: 1 / Fragment: UNP residues 31-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NG80-2 / Gene: nirK, GTNG_0650 / Plasmid: pET22b / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-MPD / ( | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate, 5.5%(w/v) PEG 4000, 0.075M CuSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. obs: 87653 / % possible obs: 92.8 % / Redundancy: 3 % / Net I/σ(I): 11.3 |
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Processing
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Refinement | Resolution: 1.34→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.301 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / 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: 14.119 Å2
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Refinement step | Cycle: 1 / Resolution: 1.34→50 Å
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Refine LS restraints |
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