+Open data
-Basic information
Entry | Database: PDB / ID: 8yrc | ||||||
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Title | Chlorinated YabJ from Staphylococcus aureus | ||||||
Components | Translation initiation inhibitor homologue | ||||||
Keywords | STRUCTURAL PROTEIN / ribonuclease / stress-response protein | ||||||
Function / homology | RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / OXYGEN ATOM / Translation initiation inhibitor homologue Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Jeong, C. / Kim, H.J. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: YabJ from Staphylococcus aureus entraps chlorides within its pocket. Authors: Jeong, C. / Kim, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yrc.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yrc.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 8yrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yrc_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8yrc_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8yrc_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 8yrc_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/8yrc ftp://data.pdbj.org/pub/pdb/validation_reports/yr/8yrc | HTTPS FTP |
-Related structure data
Related structure data | 5yu2S 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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Unit cell |
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-Components
#1: Protein | Mass: 14276.385 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: MKIINTTRLPEALGPYSHATVVNGMVYTSGQIPLNVDGKIVSADVQAQTKQVLENLKVVL EEAGSDLNSVAKATIFIKDMNDFQKINEVYGQYFNEHKPARSCVEVARLPKDVKVEIELV SKIKEL Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Gene: SAV0497 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JTJ5 #2: Chemical | ChemComp-O / | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #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: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG3350 and 100 mM Tris/HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 4, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.95 Å / Num. obs: 46373 / % possible obs: 97.6 % / Redundancy: 1.8 % / CC1/2: 0.99 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 2847 / CC1/2: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YU2 Resolution: 1.7→32.51 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.896 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.531 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→32.51 Å
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