+Open data
-Basic information
Entry | Database: PDB / ID: 5szd | ||||||
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Title | Crystal structure of Aquifex aeolicus Hfq at 1.5A | ||||||
Components | RNA-binding protein Hfq | ||||||
Keywords | RNA BINDING PROTEIN / Hfq / Aquifex / RNA-binding | ||||||
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 | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å | ||||||
Authors | Stanek, K. / Patterson, J. / Randolph, P.S. / Mura, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Authors: Stanek, K.A. / Patterson-West, J. / Randolph, P.S. / Mura, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5szd.cif.gz | 398 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5szd.ent.gz | 331.9 KB | Display | PDB format |
PDBx/mmJSON format | 5szd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/5szd ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5szd | HTTPS FTP |
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-Related structure data
Related structure data | 5szeC 1u1sS 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 9497.957 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: hfq, aq_108, aq_108B / Production host: Escherichia coli (E. coli) / References: UniProt: O66512 |
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-Non-polymers , 6 types, 457 molecules
#2: Chemical | ChemComp-MRD / ( #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-GAI / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-PEG / #7: 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: 2.05 Å3/Da / Density % sol: 40.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: sodium cacodylate, PEG 8000, MPD, 0.1 M hexamminecobalt(III) chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→57.27 Å / Num. obs: 138120 / % possible obs: 93.7 % / Redundancy: 2.2 % / Net I/σ(I): 14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U1S Resolution: 1.494→46.351 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.494→46.351 Å
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Refine LS restraints |
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LS refinement shell |
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