+Open data
-Basic information
Entry | Database: PDB / ID: 4qvd | ||||||
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Title | E.coli Hfq in complex with RNA Ads | ||||||
Components |
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Keywords | RNA binding protein/RNA / SM fold / RNA chaperone / RNA / RNA binding protein-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 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 | 4qvd.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qvd.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/4qvd ftp://data.pdbj.org/pub/pdb/validation_reports/qv/4qvd | HTTPS FTP |
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-Related structure data
Related structure data | 4qvcC 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: 2212.419 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: 2.44 Å3/Da / Density % sol: 49.53 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 16% MPEG5000, 0.1M Hepes, pH 7.2, 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: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2012 |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.972→58.19 Å / Num. all: 32548 / Num. obs: 29189 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.972→2.08 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 7.7 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HK9 Resolution: 1.972→34.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.468 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.162 / 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 mean: 28.311 Å2
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Refinement step | Cycle: LAST / Resolution: 1.972→34.13 Å
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Refine LS restraints |
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