+Open data
-Basic information
Entry | Database: PDB / ID: 3qo3 | ||||||
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Title | Crystal structure of Escherichia coli Hfq, in complex with ATP | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / SM-LIKE / PLEIOTROPIC REGULATOR / RNA CHAPERONE / ATP-BINDING | ||||||
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 / Resolution: 2.15 Å | ||||||
Authors | Beich-Frandsen, M. / Vecerek, B. / Hammele, H. / Kloiber, K. / Sjoeblom, B. / Blasi, U. / Djinovic-Carugo, K. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq Authors: Hammerle, H. / Beich-Frandsen, M. / Vecerek, B. / Rajkowitsch, L. / Carugo, O. / Djinovic-Carugo, K. / Blasi, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qo3.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qo3.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qo3 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qo3 | HTTPS FTP |
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-Related structure data
Related structure data | 1hk9S 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: N-terminal (L)Sm core-domain, UNP residues 1-65 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4172, hfq, JW4130 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6X3 #2: Chemical | ChemComp-ATP / #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: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes, 10% (W/V) PEG 8000, 8% (V/V) Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→98.67 Å / Num. all: 22913 / Num. obs: 21783 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 5.61 % / Biso Wilson estimate: 34.05 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.96 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 5.62 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1484 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HK9 Resolution: 2.15→19.89 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.967 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.22 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.687 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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