+Open data
-Basic information
Entry | Database: PDB / ID: 3gib | ||||||
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Title | Crystal Structure of the Complex of the E. coli Hfq with Poly(A) | ||||||
Components |
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Keywords | RNA binding protein/RNA / RNA binding protein / Hfq-RNA complex / degradosome component / DNA-binding / RNA-binding / Stress response / RNA binding protein-RNA COMPLEX | ||||||
Function / homology | Function and homology information sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Link, T.M. / Valentin-Hansen, P. / Brennan, R.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structure of Escherichia coli Hfq bound to polyriboadenylate RNA Authors: Link, T.M. / Valentin-Hansen, P. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gib.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gib.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gib ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gib | HTTPS FTP |
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-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: 7634.875 Da / Num. of mol.: 3 / Fragment: N-terminal fragment (2-69) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4172, hfq, JW4130 / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 null hfq / References: UniProt: P0A6X3 #2: RNA chain | | Mass: 2917.895 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45.01 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 9.5 Details: 40% MPD, 0.1 M CHES 9.5, hanging drop, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→89.087 Å / Num. obs: 9714 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.142 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.383 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 129.26 Å2 / Biso mean: 61.557 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→44.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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