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- PDB-8rvm: Crystal structure of octaheme nitrite reductase from Trichlorobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rvm | ||||||
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Title | Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P63 | ||||||
![]() | Octaheme nitrite c cytochrome c reductase | ||||||
![]() | OXIDOREDUCTASE / octaheme nitrite reductase / wild-type | ||||||
Function / homology | HEME C / PHOSPHATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Polyakov, K.M. / Safoonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P63 Authors: Polyakov, K.M. / Safoonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 55493.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
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#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 17-20 % PEG 3350, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→98.9 Å / Num. obs: 59330 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC1/2: 0.888 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.6→1.74 Å / Num. unique obs: 4437 / CC1/2: 0.656 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.496 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→98.9 Å
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Refine LS restraints |
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LS refinement shell |
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