+Open data
-Basic information
Entry | Database: PDB / ID: 3qhs | ||||||
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Title | Crystal structure of full-length Hfq from Escherichia coli | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / SM-LIKE / PLEIOTROPIC REGULATOR | ||||||
Function / homology | Function and homology information sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / RNA folding chaperone / regulation of translation, ncRNA-mediated / 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: 2.85 Å | ||||||
Authors | Beich-Frandsen, M. / Vecerek, B. / Sjoeblom, B. / Blaesi, U. / Djinovic-Carugo, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structural analysis of full-length Hfq from Escherichia coli Authors: Beich-Frandsen, M. / Vecerek, B. / Sjoblom, B. / Blasi, U. / Djinovic-Carugo, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qhs.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qhs.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qhs_validation.pdf.gz | 513 KB | Display | wwPDB validaton report |
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Full document | 3qhs_full_validation.pdf.gz | 525.5 KB | Display | |
Data in XML | 3qhs_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 3qhs_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qhs ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qhs | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 11179.354 Da / Num. of mol.: 12 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: 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: 37.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% v/v PEG 550 MME, 0.05M calcium chloride dihydrate, 0.1M BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.933 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2010 |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→80 Å / Num. all: 23985 / Num. obs: 23973 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.03 % / Biso Wilson estimate: 25.33 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 14.22 |
Reflection shell | Resolution: 2.85→2.92 Å / Redundancy: 6.43 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.6 / Num. unique all: 9573 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HK9 Resolution: 2.85→45.214 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.483 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.979 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→45.214 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Total num. of bins used: 20 /
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