+Open data
-Basic information
Entry | Database: PDB / ID: 6k6w | ||||||
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Title | Structure of RNase J2 from Staphylococcus epidermidis | ||||||
Components | Ribonuclease J 2 | ||||||
Keywords | METAL BINDING PROTEIN / Ribonuclease RNase J2 | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus epidermidis ATCC 12228 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Raj, R. / Gopal, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structure of RNase J1 from Staphylococcus epidermidis Authors: Raj, R. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k6w.cif.gz | 347.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k6w.ent.gz | 276.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/6k6w ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k6w | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64379.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis ATCC 12228 (bacteria) Strain: ATCC 12228 / Gene: rnj2 / Production host: Escherichia coli (E. coli) References: UniProt: Q8CST0, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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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: 1.9 Å3/Da / Density % sol: 35.35 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 100mM tri-sodium citrate dihydrate pH 5.6, 20% PEG 4000, 20% Isopropanol, 40% Formamide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.39 Å / Num. obs: 47771 / % possible obs: 90.6 % / Redundancy: 5.6 % / CC1/2: 0.986 / Rsym value: 0.143 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.5→2.7 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 3949 / CC1/2: 0.744 / Rsym value: 0.719 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→36.39 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→36.39 Å
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Refine LS restraints |
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LS refinement shell |
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