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Yorodumi- PDB-6yo9: Product bound structure of the Ectoine utilization protein EutD (... -
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-Basic information
Entry | Database: PDB / ID: 6yo9 | ||||||
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Title | Product bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata | ||||||
Components | Ectoine hydrolase DoeA | ||||||
Keywords | HYDROLASE / EutE / ADABA / ectoine / compatible solutes | ||||||
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: 2.4 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 | 6yo9.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yo9.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yo9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6yo9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6yo9_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6yo9_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/6yo9 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/6yo9 | HTTPS FTP |
-Related structure data
Related structure data | 6twjSC 6twkC 6twlC 6twmC 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 | #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: 4.25 Å3/Da / Density % sol: 71.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate, 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2019 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.399→50 Å / Num. obs: 60665 / % possible obs: 99.14 % / Redundancy: 14.7 % / Biso Wilson estimate: 46.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1901 / Rpim(I) all: 0.05096 / Net I/σ(I): 12.02 |
Reflection shell | Resolution: 2.399→2.484 Å / Num. unique obs: 5767 / CC1/2: 0.766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TWJ Resolution: 2.4→19.39 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 52.4 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.39 Å
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Refine LS restraints |
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