[English] 日本語
Yorodumi- PDB-8z77: The structure of thiocyanate dehydrogenase from Pelomicrobium met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8z77 | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH), activated by crystals soaking with 1 mM CuCl2 and Na ascorbate during 12 hours | ||||||
Components | Twin-arginine translocation signal domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / Thiocyanate dehydrogenase / Copper incorporation in the active site / Copper enzyme / trinuclear copper center / Activation by crystals soaking / pmTcDH / Pelomicrobium methylotrophicum / 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 / COPPER (II) ION / Twin-arginine translocation signal domain-containing protein Function and homology information | ||||||
Biological species | Pelomicrobium methylotrophicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Varfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Dergousova, N.I. / Minyaev, M.E. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH), activated by crystals soaking with 1 mM CuCl2 and Na ascorbate during 12 hours Authors: Varfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Dergousova, N.I. / Minyaev, M.E. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8z77.cif.gz | 544.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8z77.ent.gz | 446.2 KB | Display | PDB format |
PDBx/mmJSON format | 8z77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/8z77 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/8z77 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8q9xS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-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-CU / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.33 % |
---|---|
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 |
---|---|
Diffraction source | Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 26, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.71 Å / Num. obs: 93349 / % possible obs: 99.6 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.043 / Rrim(I) all: 0.156 / Χ2: 0.97 / Net I/σ(I): 14.2 / Num. measured all: 1212793 |
Reflection shell | Resolution: 2→2.03 Å / % possible obs: 96.5 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.559 / Num. measured all: 45717 / Num. unique obs: 4421 / CC1/2: 0.827 / Rpim(I) all: 0.179 / Rrim(I) all: 0.589 / Χ2: 0.95 / Net I/σ(I) obs: 4.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8Q9X Resolution: 2→23.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.21 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.198 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→23.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|