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Yorodumi- PDB-7y7o: Crystal structure of metallo-endoribonuclease YbeY from Staphyloc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y7o | ||||||
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Title | Crystal structure of metallo-endoribonuclease YbeY from Staphylococcus aureus | ||||||
Components | Endoribonuclease YbeY | ||||||
Keywords | HYDROLASE / RNA / endoribonuclease / metalloprotein / zinc | ||||||
Function / homology | Function and homology information RNA endonuclease activity / metalloendopeptidase activity / rRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Lee, J. / Ha, N.-C. | ||||||
Funding support | 1items
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Citation | Journal: J Microbiol Biotechnol. / Year: 2023 Title: Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus. Authors: Lee, J. / Jo, I. / Kwon, A.R. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y7o.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y7o.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 7y7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/7y7o ftp://data.pdbj.org/pub/pdb/validation_reports/y7/7y7o | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18871.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: Mu50 / ATCC 700699 / Gene: ybeY, SAV1570 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P67136, Hydrolases; Acting on ester bonds | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 71.26 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium citrate (pH 5.5), 40% (v/v) PEG 400, 1 mM Zinc sulfate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.28176 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28176 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 22303 / % possible obs: 96.6 % / Redundancy: 21.1 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.012 / Rrim(I) all: 0.055 / Net I/σ(I): 56 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 18.8 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 14.6 / Num. unique obs: 1017 / CC1/2: 0.988 / CC star: 0.997 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→43.59 Å / SU ML: 0.2008 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.3305 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.59 Å
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Refine LS restraints |
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LS refinement shell |
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