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- PDB-2e80: Cytochrome c Nitrite Reductase from Wolinella succinogenes with b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2.0E+80 | ||||||
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Title | Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound substrate nitrite | ||||||
![]() | Cytochrome c-552 | ||||||
![]() | OXIDOREDUCTASE / multiheme cytochrome / nitrite reductase / substrate complex | ||||||
Function / homology | ![]() nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / : / nitrate assimilation / outer membrane-bounded periplasmic space / calcium ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Einsle, O. / Kroneck, P.M.H. | ||||||
![]() | ![]() Title: Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase Authors: Einsle, O. / Messerschmidt, A. / Huber, R. / Kroneck, P.M.H. / Neese, F. #1: ![]() Title: Structure of cytochrome c nitrite reductase Authors: Einsle, O. / Messerschmidt, A. / Stach, P. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. / Kroneck, P.M.H. #2: ![]() Title: Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs Authors: Einsle, O. / Stach, P. / Messerschmidt, A. / Simon, J. / Kroeger, A. / Huber, R. / Kroneck, P.M.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.8 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 741 KB | Display | ![]() |
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Full document | ![]() | 751 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e81C ![]() 1fs7S S: Starting model for refinement 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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Details | Biological unit is a dimer, the second part is generated by the crystallographic twofold. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55343.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q9S1E5, nitrite reductase (cytochrome; ammonia-forming) |
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-Non-polymers , 6 types, 666 molecules ![](data/chem/img/NO2.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/YT3.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/YT3.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NO2 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | #6: Chemical | ChemComp-HEM / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 12% PEG 4000, 0.2M ammonium sulfate, 0.015M yttrium chloride, 0.1M sodium acetate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 10, 2001 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 90184 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FS7 Resolution: 1.6→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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