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Yorodumi- PDB-8q9y: The structure of thiocyanate dehydrogenase from Pelomicrobium met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q9y | ||||||
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Title | The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 A resolution | ||||||
Components | Twin-arginine translocation signal domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / Thiocyanate dehydrogenase / copper enzyme / trinuclear copper center / atomic resolution / conformational changes / complex with inhibitor / thiourea / Pelomicrobium methylotrophicum | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pelomicrobium methylotrophicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Varfolomeeva, L.A. / Polyakov, K.M. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum at atomic resolution Authors: Varfolomeeva, L.A. / Polyakov, K.M. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / 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 | 8q9y.cif.gz | 583.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q9y.ent.gz | 483.1 KB | Display | PDB format |
PDBx/mmJSON format | 8q9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q9y_validation.pdf.gz | 7.3 MB | Display | wwPDB validaton report |
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Full document | 8q9y_full_validation.pdf.gz | 7.3 MB | Display | |
Data in XML | 8q9y_validation.xml.gz | 48.9 KB | Display | |
Data in CIF | 8q9y_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/8q9y ftp://data.pdbj.org/pub/pdb/validation_reports/q9/8q9y | HTTPS FTP |
-Related structure data
Related structure data | 8q9xC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54093.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pelomicrobium methylotrophicum (bacteria) Gene: FR698_09980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C7ETD9 #2: Chemical | #3: Chemical | ChemComp-TOU / | #4: Chemical | ChemComp-CU / #5: 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: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→50 Å / Num. obs: 357145 / % possible obs: 93 % / Redundancy: 2.8 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.03 / Net I/σ(I): 17.52 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→39.17 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.756 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.204 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→39.17 Å
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Refine LS restraints |
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