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Yorodumi- PDB-5new: RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 5new | ||||||
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Title | RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer | ||||||
Components |
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Keywords | RNA / Hfq sRNA RNA-RNA interaction base stacking | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli S88 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.511 Å | ||||||
Authors | Schulz, E.C. / Barabas, O. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Authors: Schulz, E.C. / Seiler, M. / Zuliani, C. / Voigt, F. / Rybin, V. / Pogenberg, V. / Mucke, N. / Wilmanns, M. / Gibson, T.J. / Barabas, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5new.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5new.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 5new.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5new_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
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Full document | 5new_full_validation.pdf.gz | 477 KB | Display | |
Data in XML | 5new_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 5new_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5new ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5new | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 11179.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli S88 (bacteria) / Gene: hfq, ECS88_4758 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7MKX6 #2: RNA chain | | Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: RNA chain | | Mass: 567.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #4: Chemical | ChemComp-SO4 / #5: 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: 1.97 Å3/Da / Density % sol: 37.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1 M phosphate-citrate buffer pH 4.2, 27% PEG 1000, and 0.2 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979681 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979681 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→40.6 Å / Num. obs: 6816 / % possible obs: 96.8 % / Redundancy: 4.6 % / Net I/σ(I): 15.03 |
-Processing
Software |
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Refinement | Resolution: 2.511→40.6 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 44.329 Å2 / ksol: 0.392 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.511→40.6 Å
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Refine LS restraints |
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LS refinement shell |
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