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Yorodumi- PDB-6sji: The structure of thiocyanate dehydrogenase from Thioalkalivibrio ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sji | ||||||
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Title | The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with His 482 replaced by Gln | ||||||
Components | thiocyanate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / THIOCYANATE DEHYDROGENASE / COPPER CENTERS | ||||||
Function / homology | Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / COPPER (II) ION / Twin-arginine translocation signal domain-containing protein Function and homology information | ||||||
Biological species | Thioalkalivibrio paradoxus ARh 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Polyakov, K.M. / Tikhonova, T.V. / Rakitina, T.V. / Osipov, E. / Popov, V.O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. Authors: Tikhonova, T.V. / Sorokin, D.Y. / Hagen, W.R. / Khrenova, M.G. / Muyzer, G. / Rakitina, T.V. / Shabalin, I.G. / Trofimov, A.A. / Tsallagov, S.I. / 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 | 6sji.cif.gz | 405.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sji.ent.gz | 316.8 KB | Display | PDB format |
PDBx/mmJSON format | 6sji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sji_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
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Full document | 6sji_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 6sji_validation.xml.gz | 74.8 KB | Display | |
Data in CIF | 6sji_validation.cif.gz | 109.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/6sji ftp://data.pdbj.org/pub/pdb/validation_reports/sj/6sji | HTTPS FTP |
-Related structure data
Related structure data | 6g50C 6i3qC 6uweC 5oexS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51961.461 Da / Num. of mol.: 4 / Mutation: Q482H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria) Gene: THITH_13335 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W0DP94 #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.17M Ammonium acetate, 0.085 M Sodium cacjdilate pH 6.5, 25.5 % v/v Polyatilen glycol 8000, 15% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968623 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968623 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→90 Å / Num. obs: 176251 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / CC1/2: 0.987 / Rrim(I) all: 0.122 / Net I/σ(I): 6.63 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 13136 / CC1/2: 0.824 / Rrim(I) all: 0.456 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OEX Resolution: 1.8→89.97 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.105 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→89.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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