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Yorodumi- PDB-6twk: Substrate bound structure of the Ectoine utilization protein EutD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6twk | ||||||
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Title | Substrate bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata | ||||||
Components | Ectoine hydrolase DoeA | ||||||
Keywords | HYDROLASE / Pita bread / ectoine degradation | ||||||
Function / homology | Function and homology information ectoine hydrolase / ectoine catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Halomonas elongata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Mais, C.-N. / Altegoer, F. / Bange, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex. Authors: Mais, C.N. / Hermann, L. / Altegoer, F. / Seubert, A. / Richter, A.A. / Wernersbach, I. / Czech, L. / Bremer, E. / Bange, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6twk.cif.gz | 182.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6twk.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 6twk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/6twk ftp://data.pdbj.org/pub/pdb/validation_reports/tw/6twk | HTTPS FTP |
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-Related structure data
Related structure data | 6twjSC 6twlC 6twmC 6yo9C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44995.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halomonas elongata (bacteria) / Gene: doeA, A8U91_03446, DKQ62_09665 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1B8NWR1, UniProt: E1V7W1*PLUS, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | ChemComp-P4B / ( | #3: Chemical | ChemComp-4CS / ( | #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: 4.17 Å3/Da / Density % sol: 70.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate, 20% (wt/vol) PEG 3350 / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873127 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.42 Å / Num. obs: 78809 / % possible obs: 99.96 % / Redundancy: 8.9 % / Biso Wilson estimate: 34.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1474 / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 2.2→2.279 Å / Rmerge(I) obs: 1.466 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 6599 / CC1/2: 0.583 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TWJ Resolution: 2.25→43.88 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 38.52 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→43.88 Å
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Refine LS restraints |
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