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Yorodumi- PDB-5f6c: The structure of E. coli RNase E catalytically inactive mutant wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f6c | ||||||
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Title | The structure of E. coli RNase E catalytically inactive mutant with RNA bound | ||||||
Components |
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Keywords | HYDROLASE / ribonuclease / hydrolytic mechanism / regulatory RNA | ||||||
Function / homology | Function and homology information regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing ...regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / rRNA binding / molecular adaptor activity / magnesium ion binding / RNA binding / zinc ion binding / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å | ||||||
Authors | Bandyra, K.J. / Luisi, B.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol. Cell / Year: 2018 Title: Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E. Authors: Bandyra, K.J. / Wandzik, J.M. / Luisi, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f6c.cif.gz | 387.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f6c.ent.gz | 326.9 KB | Display | PDB format |
PDBx/mmJSON format | 5f6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f6c ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f6c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Ribonuclease ... , 2 types, 2 molecules AB
#1: Protein | Mass: 57790.805 Da / Num. of mol.: 1 / Mutation: D303R,D346R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rne, ams, hmp1, b1084, JW1071 / Production host: Escherichia coli (E. coli) / References: UniProt: P21513, ribonuclease E |
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#2: Protein | Mass: 57861.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rne, ams, hmp1, b1084, JW1071 / Production host: Escherichia coli (E. coli) / References: UniProt: P21513, ribonuclease E |
-RNA chain , 2 types, 2 molecules CE
#3: RNA chain | Mass: 606.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#4: RNA chain | Mass: 951.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Non-polymers , 3 types, 4 molecules
#5: Chemical | #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2 and 20% wt/v PEG 8000. PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 3.001→120.4 Å / Num. obs: 26464 / % possible obs: 99.2 % / Redundancy: 1.9 % / Net I/σ(I): 14.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.002→54.616 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.002→54.616 Å
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Refine LS restraints |
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LS refinement shell |
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