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Yorodumi- PDB-8z76: The structure of thiocyanate dehydrogenase from Pelomicrobium met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8z76 | ||||||
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Title | The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH), activated by crystals soaking with 1 mM CuCl2 during 6 months | ||||||
Components | Twin-arginine translocation signal domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / Thiocyanate dehydrogenase / Copper enzyme / Activation by crystals soaking / Copper incorporation in the active site / Trinuclear copper center / Conformational changes in a crystal | ||||||
Function / homology | Nitrous oxide reductase, N-terminal / Quinoprotein amine dehydrogenase, beta chain-like / 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 | Pelomicrobium methylotrophicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Varfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH), activated by crystals soaking with 1 mM CuCl2 Authors: Varfolomeeva, L.A. / Solovieva, A.Y. / 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 | 8z76.cif.gz | 302.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8z76.ent.gz | 240.5 KB | Display | PDB format |
PDBx/mmJSON format | 8z76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8z76_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 8z76_full_validation.pdf.gz | 5.5 MB | Display | |
Data in XML | 8z76_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 8z76_validation.cif.gz | 86.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/8z76 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/8z76 | HTTPS FTP |
-Related structure data
Related structure data | 8q9xS S: Starting model for refinement |
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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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 54093.301 Da / Num. of mol.: 3 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 | ChemComp-EDO / #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NA / | #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: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.5, 20% PEG 8000, 8% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 125833 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.11 / Net I/σ(I): 12.69 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8Q9X Resolution: 1.8→47.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.198 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.125 / 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: 29.113 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→47.79 Å
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Refine LS restraints |
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