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Yorodumi- PDB-8rv0: Crystal structure of octaheme nitrite reductase from Trichlorobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rv0 | ||||||
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Title | Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite | ||||||
Components | Octaheme cytochrome c nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / Octaheme nitrite reductase / complex with nitrite | ||||||
Function / homology | HEME C / NITRIC OXIDE / NITRITE ION Function and homology information | ||||||
Biological species | Trichlorobacter ammonificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Polyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite Authors: Polyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rv0.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rv0.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 8rv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/8rv0 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rv0 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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
-Protein , 1 types, 1 molecules Y
#1: Protein | Mass: 55493.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichlorobacter ammonificans (bacteria) |
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-Non-polymers , 5 types, 461 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-NO / | #4: Chemical | ChemComp-NO2 / | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20 mM NaNO2, 0.1 M Bis-Tris, pH 5.7, 17-20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→49.6 Å / Num. obs: 69684 / % possible obs: 0.988 % / Redundancy: 4.4 % / CC1/2: 0.998 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.55→1.59 Å / Num. unique obs: 5157 / CC1/2: 0.788 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→49.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.768 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.172 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→49.6 Å
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Refine LS restraints |
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