+Open data
-Basic information
Entry | Database: PDB / ID: 4jri | ||||||
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Title | Crystal Structure of Escherichia coli Hfq Proximal Edge Mutant | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / Riboregulator / Post-transcriptional 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: 1.829 Å | ||||||
Authors | Robinson, K.E. / Orans, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching. Authors: Robinson, K.E. / Orans, J. / Kovach, A.R. / Link, T.M. / 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 | 4jri.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jri.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jri_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 4jri_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 4jri_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 4jri_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jri ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jri | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7673.911 Da / Num. of mol.: 4 / Fragment: UNP residues 2-69 / Mutation: F39W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hfq, b4172, JW4130 / 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: 1.98 Å3/Da / Density % sol: 38.03 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.829→24.077 Å / Num. obs: 21700 / Rsym value: 0.06 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.829→24.077 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.829→24.077 Å
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Refine LS restraints |
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LS refinement shell |
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