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- PDB-5f7a: Nitrite complex structure of copper nitrite reductase from Alcali... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f7a | ||||||
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Title | Nitrite complex structure of copper nitrite reductase from Alcaligenes faecalis determined at 293 K | ||||||
![]() | Copper-containing nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / copper / nitrite | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. ...Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Murphy, M.E.P. / Inoue, T. / Iwata, S. / Mizohata, E. | ||||||
![]() | ![]() Title: Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography Authors: Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, ...Authors: Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Murphy, M.E.P. / 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 | ![]() | 212.9 KB | Display | ![]() |
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PDB format | ![]() | 168.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yscC ![]() 4yseC ![]() 5d4hC ![]() 5d4iC ![]() 5d4jC ![]() 5f7bC ![]() 1sjmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37019.922 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1 / Details: 100 mM sodium acetate, 7% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. obs: 142491 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SJM Resolution: 1.54→48.89 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.467 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / 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: 24.986 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→48.89 Å
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Refine LS restraints |
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