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- PDB-4ysd: Room temperature structure of copper nitrite reductase from Geoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ysd | ||||||
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Title | Room temperature structure of copper nitrite reductase from Geobacillus thermodenitrificans | ||||||
![]() | 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 | ![]() | 153.6 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.1 KB | Display | ![]() |
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Full document | ![]() | 447.3 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ysaC ![]() 4ysoC ![]() 4yspC ![]() 4ysqC ![]() 4ysrC ![]() 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 on special symmetry positions |
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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-ACY / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5.5% PEG 4000, 0.1M sodium acetate, 0.075M copper sulphate, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2013 |
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→50 Å / Num. obs: 94321 / % possible obs: 99.8 % / Redundancy: 4.2 % / Net I/σ(I): 24.4 |
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Processing
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Refinement | Resolution: 1.35→26.53 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.097 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 19.929 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→26.53 Å
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Refine LS restraints |
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