+Open data
-Basic information
Entry | Database: PDB / ID: 4qvc | ||||||
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Title | E.coli Hfq in complex with RNA Aus | ||||||
Components |
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Keywords | RNA binding protein/RNA / SM fold / RNA binding / RNA / RNA binding protein-RNA complex | ||||||
Function / homology | Function and homology information regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Wang, L.J. / Wang, W.W. / Li, F.D. / Wu, J.H. / Gong, Q.G. / Shi, Y.Y. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq Authors: Wang, L.J. / Wang, W.W. / Li, F.D. / Zhang, J. / Wu, J.H. / Gong, Q.G. / Shi, Y.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qvc.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qvc.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qvc_validation.pdf.gz | 479.7 KB | Display | wwPDB validaton report |
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Full document | 4qvc_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 4qvc_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4qvc_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/4qvc ftp://data.pdbj.org/pub/pdb/validation_reports/qv/4qvc | HTTPS FTP |
-Related structure data
Related structure data | 4qvdC 1hk9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7325.554 Da / Num. of mol.: 6 / Fragment: UNP residues 1-65 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hfq / Production host: Escherichia coli (E. coli) / References: UniProt: C1IFD2 #2: RNA chain | | Mass: 2189.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in E.coli. / Source: (synth.) Escherichia coli (E. coli) #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: 2.43 Å3/Da / Density % sol: 49.3 % / Mosaicity: 0.554 ° |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12% PEG4000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→40 Å / Num. all: 31605 / Num. obs: 29582 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.105 / Χ2: 1.331 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HK9 Resolution: 1.99→33.99 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2629 / WRfactor Rwork: 0.2141 / FOM work R set: 0.8037 / SU B: 4.6 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1964 / SU Rfree: 0.1745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 81.64 Å2 / Biso mean: 34.715 Å2 / Biso min: 16.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→33.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.988→2.04 Å / Total num. of bins used: 20
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